r24005 - /branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py

[tlinnet]

Author: tlinnet
Date: Mon Jun 16 22:11:41 2014
New Revision: 24005

URL: http://svn.gna.org/viewcvs/relax?rev=24005view=rev
Log:
Fix for documentation in ns mmq 2site/sq/dq/zq/mq.

Now explains which dimension data should be in.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py?rev=24005r1=24004r2=24005view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py Mon Jun 16 
22:11:41 2014
@@ -105,31 +105,31 @@
 @keyword m2:A complex numpy matrix to be populated.
 @type m2:   numpy rank-2, 2D complex64 array
 @keyword R20A:  The transverse, spin-spin relaxation rate for 
state A.
-@type R20A: float
+@type R20A: numpy float array of rank [NS][[NM][NO][ND]
 @keyword R20B:  The transverse, spin-spin relaxation rate for 
state B.
-@type R20B: float
+@type R20B: numpy float array of rank [NS][[NM][NO][ND]
 @keyword pA:The population of state A.
 @type pA:   float
 @keyword pB:The population of state B.
 @type pB:   float
 @keyword dw:The chemical exchange difference between states A 
and B in rad/s.
-@type dw:   float
+@type dw:   numpy float array of rank [NS][[NM][NO][ND]
 @keyword dwH:   The proton chemical exchange difference between 
states A and B in rad/s.
-@type dwH:  float
+@type dwH:  numpy float array of rank [NS][[NM][NO][ND]
 @keyword k_AB:  The rate of exchange from site A to B (rad/s).
 @type k_AB: float
 @keyword k_BA:  The rate of exchange from site B to A (rad/s).
 @type k_BA: float
 @keyword inv_tcpmg: The inverse of the total duration of the CPMG 
element (in inverse seconds).
-@type inv_tcpmg:float
+@type inv_tcpmg:numpy float array of rank [NS][[NM][NO][ND]
 @keyword tcp:   The tau_CPMG times (1 / 4.nu1).
-@type tcp:  numpy rank-1 float array
+@type tcp:  numpy float array of rank [NS][[NM][NO][ND]
 @keyword back_calc: The array for holding the back calculated R2eff 
values.  Each element corresponds to one of the CPMG nu1 frequencies.
-@type back_calc:numpy rank-1 float array
+@type back_calc:numpy float array of rank [NS][[NM][NO][ND]
 @keyword num_points:The number of points on the dispersion curve, 
equal to the length of the tcp and back_calc arguments.
-@type num_points:   int
+@type num_points:   numpy int array of rank [NS][[NM][NO][ND]
 @keyword power: The matrix exponential power array.
-@type power:numpy int16, rank-1 array
+@type power:numpy int array of rank [NS][[NM][NO][ND]
 
 
 # Extract shape of experiment.
@@ -254,31 +254,31 @@
 @keyword m2:A complex numpy matrix to be populated.
 @type m2:   numpy rank-2, 2D complex64 array
 @keyword R20A:  The transverse, spin-spin relaxation rate for 
state A.
-@type R20A: float
+@type R20A: numpy float array of rank [NS][[NM][NO][ND]
 @keyword R20B:  The transverse, spin-spin relaxation rate for 
state B.
-@type R20B: float
+@type R20B: numpy float array of rank [NS][[NM][NO][ND]
 @keyword pA:The population of state A.
 @type pA:   float
 @keyword pB:The population of state B.
 @type pB:   float
 @keyword dw:The combined chemical exchange difference between 
states A and B in rad/s.  It should be set to dwH for 1H SQ data, dw for 
heteronuclear SQ data, dwH-dw for ZQ data, and dwH+dw for DQ data.
-@type dw:   float
+@type dw:   numpy float array of rank [NS][[NM][NO][ND]
 @keyword dwH:   Unused - this is simply to match the 
r2eff_ns_mmq_2site_mq() function arguments.
-@type dwH:  float
+@type dwH:  numpy float array of rank [NS][[NM][NO][ND]
 @keyword k_AB:  The rate of exchange from site A to B (rad/s).
 @type k_AB: float
 @keyword k_BA:  The rate of exchange from site B to A (rad/s).
 @type k_BA: float
 @keyword inv_tcpmg: The inverse of the total duration of the CPMG 
element (in inverse seconds).
-@type inv_tcpmg:float
+@type

r24001 - /branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py

[tlinnet]

Author: tlinnet
Date: Mon Jun 16 22:11:33 2014
New Revision: 24001

URL: http://svn.gna.org/viewcvs/relax?rev=24001view=rev
Log:
Changed unit test of MMQ CR72 to pass.

dw needs to be of numpy structure.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py

Modified: 
branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py?rev=24001r1=24000r2=24001view=diff
==
--- 
branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
(original)
+++ 
branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
Mon Jun 16 22:11:33 2014
@@ -20,7 +20,7 @@
 ###
 
 # Python module imports.
-from numpy import array, float64, int16, pi, zeros
+from numpy import array, float64, int16, ones, pi, zeros
 from unittest import TestCase
 
 # relax module imports.
@@ -41,7 +41,7 @@
 self.kex = 1000.0
 
 # Required data structures.
-self.num_points = 7
+self.num_points = 6
 self.ncyc = array([2, 4, 8, 10, 20, 40])
 relax_times = 0.04
 self.cpmg_frqs = self.ncyc / relax_times
@@ -59,8 +59,10 @@
 # Parameter conversions.
 k_AB, k_BA, pB, dw_frq, dwH_frq = self.param_conversion(pA=self.pA, 
kex=self.kex, dw=self.dw, dwH=self.dwH, sfrq=self.sfrq)
 
+a = ones(self.ncyc.shape)
+
 # Calculate the R2eff values.
-r2eff_mmq_cr72(r20=self.r20, pA=self.pA, pB=pB, dw=dw_frq, 
dwH=dwH_frq, kex=self.kex, k_AB=k_AB, k_BA=k_BA, cpmg_frqs=self.cpmg_frqs, 
inv_tcpmg=self.inv_relax_times, tcp=self.tau_cpmg, back_calc=self.R2eff, 
num_points=self.num_points, power=self.ncyc)
+r2eff_mmq_cr72(r20=self.r20*a, pA=self.pA, pB=pB, dw=dw_frq*a, 
dwH=dwH_frq*a, kex=self.kex, k_AB=k_AB, k_BA=k_BA, cpmg_frqs=self.cpmg_frqs, 
inv_tcpmg=self.inv_relax_times, tcp=self.tau_cpmg, back_calc=self.R2eff)
 
 # Check all R2eff values.
 for i in range(self.num_points):
@@ -184,10 +186,10 @@
 
 
 def test_mmq_cr72_no_rex8(self):
-Test the r2eff_mmq_cr72() function for no exchange when kex = 
1e5.
+Test the r2eff_mmq_cr72() function for no exchange when kex = 
1e8.
 
 # Parameter reset.
-self.kex = 1e5
+self.kex = 1e8
 
 # Calculate and check the R2eff values.
 self.calc_r2eff()


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r24003 - /branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py

[tlinnet]

Author: tlinnet
Date: Mon Jun 16 22:11:38 2014
New Revision: 24003

URL: http://svn.gna.org/viewcvs/relax?rev=24003view=rev
Log:
Modified lib function for NS MMQ 2site, to have looping over spins and 
frequencies inside lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py?rev=24003r1=24002r2=24003view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py Mon Jun 16 
22:11:38 2014
@@ -132,91 +132,107 @@
 @type power:numpy int16, rank-1 array
 
 
-# Populate the m1 and m2 matrices (only once per function call for speed).
-populate_matrix(matrix=m1, R20A=R20A, R20B=R20B, dw=-dw-dwH, k_AB=k_AB, 
k_BA=k_BA) # D+ matrix component.
-populate_matrix(matrix=m2, R20A=R20A, R20B=R20B, dw=dw-dwH, k_AB=k_AB, 
k_BA=k_BA)# Z- matrix component.
-
-# Loop over the time points, back calculating the R2eff values.
-for i in range(num_points):
-# The M1 and M2 matrices.
-M1 = matrix_exponential(m1*tcp[i])# Equivalent to D+.
-M2 = matrix_exponential(m2*tcp[i])# Equivalent to Z-.
-
-# The complex conjugates M1* and M2*
-M1_star = conj(M1)# Equivalent to D+*.
-M2_star = conj(M2)# Equivalent to Z-*.
-
-# Repetitive dot products (minimised for speed).
-M1_M2 = dot(M1, M2)
-M2_M1 = dot(M2, M1)
-M1_M2_M2_M1 = dot(M1_M2, M2_M1)
-M2_M1_M1_M2 = dot(M2_M1, M1_M2)
-M1_M2_star = dot(M1_star, M2_star)
-M2_M1_star = dot(M2_star, M1_star)
-M1_M2_M2_M1_star = dot(M1_M2_star, M2_M1_star)
-M2_M1_M1_M2_star = dot(M2_M1_star, M1_M2_star)
-
-# Special case of 1 CPMG block - the power is zero.
-if power[i] == 1:
-# M1.M2.
-A = M1_M2
-
-# M1*.M2*.
-B = M1_M2_star
-
-# M2.M1.
-C = M2_M1
-
-# M2*.M1*.
-D = M2_M1_star
-
-# Matrices for even number of CPMG blocks.
-elif power[i] % 2 == 0:
-# The power factor (only calculate once).
-fact = int(floor(power[i] / 2))
-
-# (M1.M2.M2.M1)^(n/2).
-A = square_matrix_power(M1_M2_M2_M1, fact)
-
-# (M2*.M1*.M1*.M2*)^(n/2).
-B = square_matrix_power(M2_M1_M1_M2_star, fact)
-
-# (M2.M1.M1.M2)^(n/2).
-C = square_matrix_power(M2_M1_M1_M2, fact)
-
-# (M1*.M2*.M2*.M1*)^(n/2).
-D = square_matrix_power(M1_M2_M2_M1_star, fact)
-
-# Matrices for odd number of CPMG blocks.
-else:
-# The power factor (only calculate once).
-fact = int(floor((power[i] - 1) / 2))
-
-# (M1.M2.M2.M1)^((n-1)/2).M1.M2.
-A = square_matrix_power(M1_M2_M2_M1, fact)
-A = dot(A, M1_M2)
-
-# (M1*.M2*.M2*.M1*)^((n-1)/2).M1*.M2*.
-B = square_matrix_power(M1_M2_M2_M1_star, fact)
-B = dot(B, M1_M2_star)
-
-# (M2.M1.M1.M2)^((n-1)/2).M2.M1.
-C = square_matrix_power(M2_M1_M1_M2, fact)
-C = dot(C, M2_M1)
-
-# (M2*.M1*.M1*.M2*)^((n-1)/2).M2*.M1*.
-D = square_matrix_power(M2_M1_M1_M2_star, fact)
-D = dot(D, M2_M1_star)
-
-# The next lines calculate the R2eff using a two-point approximation, 
i.e. assuming that the decay is mono-exponential.
-A_B = dot(A, B)
-C_D = dot(C, D)
-Mx = dot(dot(F_vector, (A_B + C_D)), M0)
-Mx = Mx.real / 2.0
-if Mx = 0.0 or isNaN(Mx):
-back_calc[i] = 1e99
-else:
-back_calc[i]= -inv_tcpmg[i] * log(Mx / pA)
+# Extract shape of experiment.
+NS, NM, NO = num_points.shape
+
+# Loop over spins.
+for si in range(NS):
+# Loop over the spectrometer frequencies.
+for mi in range(NM):
+# Loop over offsets:
+for oi in range(NO):
+
+r20a_si_mi_oi = R20A[si][mi][oi][0]
+r20b_si_mi_oi = R20B[si][mi][oi][0]
+dw_si_mi_oi = dw[si][mi][oi][0]
+dwH_si_mi_oi = dwH[si][mi][oi][0]
+num_points_si_mi_oi = num_points[si][mi][oi]
+
+# Populate the m1 and m2 matrices (only once per function call 
for speed).
+populate_matrix(matrix=m1, R20A=r20a_si_mi_oi, 
R20B=r20b_si_mi_oi, dw=-dw_si_mi_oi - dwH_si_mi_oi, k_AB=k_AB, k_BA=k_BA) # 
D+ matrix component.
+populate_matrix(matrix=m2, R20A=r20a_si_mi_oi, 
R20B=r20b_si_mi_oi, dw=dw_si_mi_oi

r24007 - /branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py

[tlinnet]

Author: tlinnet
Date: Mon Jun 16 22:11:56 2014
New Revision: 24007

URL: http://svn.gna.org/viewcvs/relax?rev=24007view=rev
Log:
Changed the calculation of inner product in model ns cpmg 2site 3d.

The out argument of numpy.dot is buggy, and should not be used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py?rev=24007r1=24006r2=24007view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py Mon Jun 16 
22:11:56 2014
@@ -141,9 +141,6 @@
 # The matrix R that contains all the contributions to the 
evolution, i.e. relaxation, exchange and chemical shift evolution.
 R = rcpmg_3d(R1A=r10a, R1B=r10b, R2A=R2A_si_mi, R2B=R2B_si_mi, 
pA=pA, pB=pB, dw=dw_si_mi, k_AB=k_AB, k_BA=k_BA)
 
-# The essential evolution matrix. This initialises the structure.
-evolution_matrix = asarray(R) * 0.0
-
 # Loop over the time points, back calculating the R2eff values.
 for di in range(num_points_si_mi):
 # Extract the values from the higher dimensional arrays.
@@ -160,10 +157,10 @@
 
 # The essential evolution matrix.
 # This is the first round.
-dot(Rexpo, r180x, evolution_matrix)
-dot(evolution_matrix * 1.0, Rexpo, evolution_matrix)
+evolution_matrix = dot(Rexpo, r180x)
+evolution_matrix = dot(evolution_matrix, Rexpo)
 # The second round.
-dot(evolution_matrix * 1.0, evolution_matrix * 1.0, 
evolution_matrix)
+evolution_matrix = dot(evolution_matrix, evolution_matrix )
 
 # Loop over the CPMG elements, propagating the magnetisation.
 for j in range(power_si_mi_di):


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r24008 - /trunk/test_suite/shared_data/dispersion/profiling/profiling_cr72.txt

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 09:18:19 2014
New Revision: 24008

URL: http://svn.gna.org/viewcvs/relax?rev=24008view=rev
Log:
Adding last profiling information for model CR72.

Modified:
trunk/test_suite/shared_data/dispersion/profiling/profiling_cr72.txt

[This mail would be too long, it was shortened to contain the URLs only.]

Modified: trunk/test_suite/shared_data/dispersion/profiling/profiling_cr72.txt
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/dispersion/profiling/profiling_cr72.txt?rev=24008r1=24007r2=24008view=diff


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r24010 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 09:18:39 2014
New Revision: 24010

URL: http://svn.gna.org/viewcvs/relax?rev=24010view=rev
Log:
Added missing instances of cleaning the data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24010r1=24009r2=24010view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 
09:18:39 2014
@@ -1309,6 +1309,9 @@
 # Back calculate the R2eff values.
 r2eff_mmq_cr72(r20=r20, pA=pA, pB=pB, dw=aliased_dw, 
dwH=aliased_dwH, kex=kex, k_AB=k_AB, k_BA=k_BA, cpmg_frqs=self.cpmg_frqs[ei], 
inv_tcpmg=self.inv_relax_times[ei], tcp=self.tau_cpmg[ei], 
back_calc=self.back_calc[ei])
 
+# Clean the data for all values, which is left over at the end of 
arrays.
+self.back_calc[ei] = self.back_calc[ei]*self.disp_struct[ei]
+
 # For all missing data points, set the back-calculated value to 
the measured values so that it has no effect on the chi-squared value.
 if self.has_missing:
 # Replace with values.
@@ -1340,6 +1343,9 @@
 
 # Reshape R20 to per experiment, spin and frequency.
 self.back_calc[:] = multiply.outer( R20.reshape(self.NE, self.NS, 
self.NM), self.no_nd_ones )
+
+# Clean the data for all values, which is left over at the end of 
arrays.
+self.back_calc = self.back_calc*self.disp_struct
 
 ## For all missing data points, set the back-calculated value to the 
measured values so that it has no effect on the chi-squared value.
 if self.has_missing:
@@ -1554,6 +1560,9 @@
 # Back calculate the R2eff values for each experiment type.
 self.r2eff_ns_mmq[ei](M0=self.M0, m1=self.m1, m2=self.m2, 
R20A=r20, R20B=r20, pA=pA, pB=pB, dw=aliased_dw, dwH=aliased_dwH, k_AB=k_AB, 
k_BA=k_BA, inv_tcpmg=self.inv_relax_times[ei], tcp=self.tau_cpmg[ei], 
back_calc=self.back_calc[ei], num_points=self.num_disp_points[ei], 
power=self.power[ei])
 
+# Clean the data for all values, which is left over at the end of 
arrays.
+self.back_calc[ei] = self.back_calc[ei]*self.disp_struct[ei]
+
 # For all missing data points, set the back-calculated value to 
the measured values so that it has no effect on the chi-squared value.
 if self.has_missing:
 # Replace with values.
@@ -1811,7 +1820,6 @@
 return chi2_rankN(self.values, self.back_calc, self.errors)
 
 
-
 def func_TSMFK01(self, params):
 Target function for the the Tollinger et al. (2001) 2-site 
very-slow exchange model, range of microsecond to second time scale.
 


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r24009 - /trunk/test_suite/system_tests/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 09:18:24 2014
New Revision: 24009

URL: http://svn.gna.org/viewcvs/relax?rev=24009view=rev
Log:
Added systemtest for model LM63 3 site.

According to results folder in:
test_suite/shared_data/dispersion/Hansen/relax_results/LM63 3-site

This should pass.

But i doesnt?

Modified:
trunk/test_suite/system_tests/relax_disp.py

Modified: trunk/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=24009r1=24008r2=24009view=diff
==
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Tue Jun 17 09:18:24 2014
@@ -2492,6 +2492,70 @@
 self.assertAlmostEqual(spin71.phi_ex, 0.0553787828347638)
 self.assertAlmostEqual(spin71.kex/1000, 2781.72293906248/1000)
 self.assertAlmostEqual(spin71.chi2, 17.0776399916287)
+
+
+def test_hansen_cpmg_data_to_lm63_3site(self):
+Optimisation of Dr. Flemming Hansen's CPMG data to the LM63 
dispersion model.
+
+This uses the data from Dr. Flemming Hansen's paper at 
http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation 
time period.
+
+
+# Base data setup.
+self.setup_hansen_cpmg_data(model='LM63 3-site')
+
+# Alias the spins.
+spin70 = return_spin(:70)
+spin71 = return_spin(:71)
+
+# The R20 keys.
+r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
+r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
+
+## Set the initial parameter values.
+spin70.r2 = {r20_key1: 7.570370921220954, r20_key2: 8.694446951909107}
+spin70.phi_ex_B = 0.14872003058250227
+spin70.phi_ex_C = 0.1319419923472704
+spin70.kB = 4103.672910444741
+spin70.kC = 7029.001690726248
+spin71.r2 = {r20_key1: 5.1347793381636, r20_key2: 7.156573986051575}
+spin71.phi_ex_B = 0.04013553485505605
+spin71.phi_ex_C = 0.020050748406928887
+spin71.kB = 4045.3007136121364
+spin71.kC = 3586.38798270774
+
+#self.interpreter.relax_disp.r20_from_min_r2eff(force=False)
+#self.interpreter.grid_search(lower=None, upper=None, inc=41, 
constraints=True, verbosity=1)
+
+# Low precision optimisation.
+self.interpreter.minimise(min_algor='simplex', line_search=None, 
hessian_mod=None, hessian_type=None, func_tol=1e-25, grad_tol=None, 
max_iter=1000, constraints=True, scaling=True, verbosity=1)
+
+# Printout.
+print(\n\nOptimised parameters:\n)
+print(%-20s %-20s %-20s % (Parameter, Value (:70), Value 
(:71)))
+print(%-20s %20.15g %20.15g % (R2 (500 MHz), spin70.r2[r20_key1], 
spin71.r2[r20_key1]))
+print(%-20s %20.15g %20.15g % (R2 (800 MHz), spin70.r2[r20_key2], 
spin71.r2[r20_key2]))
+print(%-20s %20.15g %20.15g % (phi_ex_B, spin70.phi_ex_B, 
spin71.phi_ex_B))
+print(%-20s %20.15g %20.15g % (phi_ex_C, spin70.phi_ex_C, 
spin71.phi_ex_C))
+print(%-20s %20.15g %20.15g % (kB, spin70.kB, spin71.kB))
+print(%-20s %20.15g %20.15g % (kC, spin70.kC, spin71.kC))
+print(%-20s %20.15g %20.15g\n % (chi2, spin70.chi2, spin71.chi2))
+
+# Checks for residue :70.
+#self.assertAlmostEqual(spin70.r2[r20_key1], 6.74362294539099)
+#self.assertAlmostEqual(spin70.r2[r20_key2], 6.57406797067481, 6)
+self.assertAlmostEqual(spin70.phi_ex_B, 0.148720030582502)
+self.assertAlmostEqual(spin70.phi_ex_C, 0.13194199234727)
+self.assertAlmostEqual(spin70.kB/1000, 4103.67291044474/1000, 6)
+self.assertAlmostEqual(spin70.kC/1000, 7029.00169072625/1000, 6)
+#self.assertAlmostEqual(spin70.chi2, 363.534044873483)
+
+# Checks for residue :71.
+#self.assertAlmostEqual(spin71.r2[r20_key1], 5.00776657712558)
+self.assertAlmostEqual(spin71.phi_ex_B, 0.040135534855056)
+self.assertAlmostEqual(spin71.phi_ex_C, 0.0200507484069289)
+self.assertAlmostEqual(spin71.kB/1000, 4045.30071361214/1000)
+self.assertAlmostEqual(spin71.kC/1000, 3586.38798270774/1000)
+#self.assertAlmostEqual(spin71.chi2, 17.0776399916287)
 
 
 def test_hansen_cpmg_data_to_ns_cpmg_2site_3D(self):


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r24011 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 09:18:41 2014
New Revision: 24011

URL: http://svn.gna.org/viewcvs/relax?rev=24011view=rev
Log:
Bug fix for model LM63 3site. The index si has to be used to extract data to 
lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24011r1=24010r2=24011view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 
09:18:41 2014
@@ -1075,7 +1075,7 @@
 rex_C_scaled = rex_C[si] * self.frqs_squared[0][si][mi][0][0]
 
 # Back calculate the R2eff values.
-r2eff_LM63_3site(r20=R20[r20_index], rex_B=rex_B_scaled, 
rex_C=rex_C_scaled, quart_kB=quart_kB, quart_kC=quart_kC, 
cpmg_frqs=self.cpmg_frqs[0][mi][0], back_calc=self.back_calc[0][si][mi][0], 
num_points=self.num_disp_points[0][si][mi][0])
+r2eff_LM63_3site(r20=R20[r20_index], rex_B=rex_B_scaled, 
rex_C=rex_C_scaled, quart_kB=quart_kB, quart_kC=quart_kC, 
cpmg_frqs=self.cpmg_frqs[0][si][mi][0], back_calc=self.back_calc[0][si][mi][0], 
num_points=self.num_disp_points[0][si][mi][0])
 
 # For all missing data points, set the back-calculated value 
to the measured values so that it has no effect on the chi-squared value.
 for di in range(self.num_disp_points[0][si][mi][0]):


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r24012 - in /branches/disp_spin_speed: ./ docs/latex/ test_suite/ test_suite/shared_data/dispersion/profiling/ test_suite/sy...

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 09:20:13 2014
New Revision: 24012

URL: http://svn.gna.org/viewcvs/relax?rev=24012view=rev
Log:
Merged revisions 23881,23945,24008-24009 via svnmerge from 
svn+ssh://tlin...@svn.gna.org/svn/relax/trunk


  r23881 | bugman | 2014-06-12 14:47:31 +0200 (Thu, 12 Jun 2014) | 8 lines
  
  Better handling of the control-C keyboard interrupt signal in the relax test 
suite.
  
  This includes two changes.  The Python 2.7 and higher 
unittest.installHandler() function is now
  called, when present, to terminate all tests using the unittest module 
control-C handler.  The
  second change is that the keyboard interrupt signal is caught in a try-except 
statement, a message
  printed out, and the tests terminated.  This should be an improvement for all 
systems.

  r23945 | bugman | 2014-06-13 17:54:50 +0200 (Fri, 13 Jun 2014) | 17 lines
  
  Reverted r23693 as SciPy is actually still used in the frame order analyses.
  
  The command used was:
  $ svn merge -r23693:r23692 .
  
  .
r23693 | bugman | 2014-06-06 14:24:44 +0200 (Fri, 06 Jun 2014) | 6 lines
Changed paths:
   M /trunk/docs/latex/install.tex

Removed all SciPy references in the installation chapter of the manual.

This is because SciPy is no longer used in the frame order analysis, hence 
it is not used for any
part of relax.
  .

  r24008 | tlinnet | 2014-06-17 09:18:19 +0200 (Tue, 17 Jun 2014) | 1 line
  
  Adding last profiling information for model CR72.

  r24009 | tlinnet | 2014-06-17 09:18:24 +0200 (Tue, 17 Jun 2014) | 8 lines
  
  Added systemtest for model LM63 3 site.
  
  According to results folder in:
  test_suite/shared_data/dispersion/Hansen/relax_results/LM63 3-site
  
  This should pass.
  
  But i doesnt?


Modified:
branches/disp_spin_speed/   (props changed)
branches/disp_spin_speed/docs/latex/install.tex

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.txt
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
branches/disp_spin_speed/test_suite/test_suite_runner.py

[This mail would be too long, it was shortened to contain the URLs only.]

Modified: branches/disp_spin_speed/docs/latex/install.tex
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/docs/latex/install.tex?rev=24012r1=24011r2=24012view=diff

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.txt
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.txt?rev=24012r1=24011r2=24012view=diff

Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24012r1=24011r2=24012view=diff

Modified: branches/disp_spin_speed/test_suite/test_suite_runner.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/test_suite_runner.py?rev=24012r1=24011r2=24012view=diff


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r24013 - /branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 09:33:32 2014
New Revision: 24013

URL: http://svn.gna.org/viewcvs/relax?rev=24013view=rev
Log:
Temporary added systemtest: test_korzhnev_2005_all_data_disp_speed_bug.

This makes a minimisation with 1 iteration, and so will give the chi2 value at 
the preset
parameter values.

This is chi2 value should give 162.5, but gives 74.7104.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24013r1=24012r2=24013view=diff
==
--- branches/disp_spin_speed/test_suite/system_tests/relax_disp.py  
(original)
+++ branches/disp_spin_speed/test_suite/system_tests/relax_disp.py  Tue Jun 
17 09:33:32 2014
@@ -3558,6 +3558,101 @@
 self.assertAlmostEqual(spin.chi2/1000, 162.511988511609/1000, 3)
 
 
+def test_korzhnev_2005_all_data_disp_speed_bug(self):
+Optimisation of all the Korzhnev et al., 2005 CPMG data using the 
'NS MMQ 2-site' model.
+
+This uses the data from Dmitry Korzhnev's paper at U{DOI: 
10.1021/ja054550ehttp://dx.doi.org/10.1021/ja054550e}.  This is the 1H SQ, 
15N SQ, ZQ, DQ, 1H MQ and 15N MQ data for residue Asp 9 of the Fyn SH3 domain 
mutant.
+
+Here all data will be optimised.  The values found by cpmg_fit using 
just this data are:
+
+- r2 = {'H-S 500':  6.671649051677150, 'H-S 600':  
6.988634195648529, 'H-S 800':  5.527971316790596,
+'N-S 500':  8.394988400015988, 'N-S 600':  
8.891359568401835, 'N-S 800': 10.405356669006709,
+'NHZ 500':  5.936446687394352, 'NHZ 600':  
6.717058062814535, 'NHZ 800':  6.838733853403030,
+'NHD 500':  8.593136215779710, 'NHD 600': 
10.651511259239674, 'NHD 800': 12.567902357560627,
+'HNM 500':  7.851325614877817, 'HNM 600':  
8.408803624020202, 'HNM 800': 11.227489645758979,
+'NHM 500':  9.189159145380575, 'NHM 600':  
9.856814478405868, 'NHM 800': 11.967910041807118},
+- pA = 0.943125351763911,
+- dw = 4.421827493809807,
+- dwH = -0.272637034755752,
+- kex = 360.609744568697238,
+- chi2 = 162.589570340050813.
+
+
+# Base data setup.
+self.setup_korzhnev_2005_data(data_list=['SQ', '1H SQ', 'DQ', 'ZQ', 
'MQ', '1H MQ'])
+
+# Alias the spin.
+spin = return_spin(:9@N)
+
+# The R20 keys.
+r20_key1  = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, 
frq=500e6)
+r20_key2  = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, 
frq=600e6)
+r20_key3  = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_SQ, 
frq=800e6)
+r20_key4  = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
+r20_key5  = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=600e6)
+r20_key6  = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
+r20_key7  = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=500e6)
+r20_key8  = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=600e6)
+r20_key9  = generate_r20_key(exp_type=EXP_TYPE_CPMG_ZQ, frq=800e6)
+r20_key10 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=500e6)
+r20_key11 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=600e6)
+r20_key12 = generate_r20_key(exp_type=EXP_TYPE_CPMG_DQ, frq=800e6)
+r20_key13 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, 
frq=500e6)
+r20_key14 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, 
frq=600e6)
+r20_key15 = generate_r20_key(exp_type=EXP_TYPE_CPMG_PROTON_MQ, 
frq=800e6)
+r20_key16 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=500e6)
+r20_key17 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=600e6)
+r20_key18 = generate_r20_key(exp_type=EXP_TYPE_CPMG_MQ, frq=800e6)
+
+# Set the initial parameter values.
+spin.r2 = {
+r20_key1:   6.67288025927458, r20_key2:   6.98951408255098, 
r20_key3:   5.52959273852704,
+r20_key4:   8.39471048876782, r20_key5:   8.89290699178799, 
r20_key6:  10.40770687236930,
+r20_key7:   5.93611174376373, r20_key8:   6.71735669582514, 
r20_key9:   6.83835225518265,
+r20_key10:  8.59615074668922, r20_key11: 10.65121378892910, 
r20_key12: 12.57108229191090,
+r20_key13:  7.85956711501608, r20_key14:  8.41891642907918, 
r20_key15: 11.23620892230380,
+r20_key16:  9.19654863789350, r20_key17:  9.86031627358462, 
r20_key18: 11.97523755925750
+}
+spin.pA = 0.943129019477673
+spin.dw = 4.42209952545181
+spin.dwH = -0.27258970590969
+spin.kex

r24014 - in /branches/disp_spin_speed/lib/dispersion: ns_cpmg_2site_3d.py ns_cpmg_2site_star.py ns_mmq_2site.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 09:47:09 2014
New Revision: 24014

URL: http://svn.gna.org/viewcvs/relax?rev=24014view=rev
Log:
Updated documentation on dimensionality of numpy array num_points.

They are in dimension [NE][NS][[NM][NO], where oi gives the number of
dispersion points at that offset.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py?rev=24014r1=24013r2=24014view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py Tue Jun 17 
09:47:09 2014
@@ -97,7 +97,7 @@
 @keyword back_calc: The array for holding the back calculated R2eff 
values.  Each element corresponds to one of the CPMG nu1 frequencies.
 @type back_calc:numpy float array of rank [NE][NS][[NM][NO][ND]
 @keyword num_points:The number of points on the dispersion curve, 
equal to the length of the tcp and back_calc arguments.
-@type num_points:   numpy int array of rank [NE][NS][[NM][NO][ND]
+@type num_points:   numpy int array of rank [NE][NS][[NM][NO]
 @keyword power: The matrix exponential power array.
 @type power:numpy int array of rank [NE][NS][[NM][NO][ND]
 

Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py?rev=24014r1=24013r2=24014view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py   
(original)
+++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py   Tue Jun 
17 09:47:09 2014
@@ -100,7 +100,7 @@
 @keyword back_calc: The array for holding the back calculated R2eff 
values.  Each element corresponds to one of the CPMG nu1 frequencies.
 @type back_calc:numpy float array of rank [NE][NS][[NM][NO][ND]
 @keyword num_points:The number of points on the dispersion curve, 
equal to the length of the tcp and back_calc arguments.
-@type num_points:   numpy int array of rank [NE][NS][[NM][NO][ND]
+@type num_points:   numpy int array of rank [NE][NS][[NM][NO]
 @keyword power: The matrix exponential power array.
 @type power:numpy int array of rank [NE][NS][[NM][NO][ND]
 

Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py?rev=24014r1=24013r2=24014view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py Tue Jun 17 
09:47:09 2014
@@ -276,7 +276,7 @@
 @keyword back_calc: The array for holding the back calculated R2eff 
values.  Each element corresponds to one of the CPMG nu1 frequencies.
 @type back_calc:numpy float array of rank [NS][[NM][NO][ND]
 @keyword num_points:The number of points on the dispersion curve, 
equal to the length of the tcp and back_calc arguments.
-@type num_points:   numpy int array of rank [NS][[NM][NO][ND]
+@type num_points:   numpy int array of rank [NS][[NM][NO]
 @keyword power: The matrix exponential power array.
 @type power:numpy int array of rank [NS][[NM][NO][ND]
 


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r24019 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 11:56:45 2014
New Revision: 24019

URL: http://svn.gna.org/viewcvs/relax?rev=24019view=rev
Log:
Moved the cleaning of data points and replacing of values of out loop for model 
ns mmq 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24019r1=24018r2=24019view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 
11:56:45 2014
@@ -1560,20 +1560,16 @@
 # Back calculate the R2eff values for each experiment type.
 self.r2eff_ns_mmq[ei](M0=self.M0, m1=self.m1, m2=self.m2, 
R20A=r20, R20B=r20, pA=pA, pB=pB, dw=aliased_dw, dwH=aliased_dwH, k_AB=k_AB, 
k_BA=k_BA, inv_tcpmg=self.inv_relax_times[ei], tcp=self.tau_cpmg[ei], 
back_calc=self.back_calc[ei], num_points=self.num_disp_points[ei], 
power=self.power[ei])
 
-# Clean the data for all values, which is left over at the end of 
arrays.
-self.back_calc[ei] = self.back_calc[ei]*self.disp_struct[ei]
-
-# For all missing data points, set the back-calculated value to 
the measured values so that it has no effect on the chi-squared value.
-if self.has_missing:
-# Replace with values.
-mask_replace_blank_ei = masked_equal(self.missing, 1.0)
-self.back_calc[mask_replace_blank_ei.mask] = 
self.values[mask_replace_blank_ei.mask]
-
-# Calculate and return the chi-squared value.
-chi2_sum += chi2_rankN(self.values[ei], self.back_calc[ei], 
self.errors[ei])
+# Clean the data for all values, which is left over at the end of 
arrays.
+self.back_calc = self.back_calc*self.disp_struct
+
+## For all missing data points, set the back-calculated value to the 
measured values so that it has no effect on the chi-squared value.
+if self.has_missing:
+# Replace with values.
+self.back_calc[self.mask_replace_blank.mask] = 
self.values[self.mask_replace_blank.mask]
 
 # Return the total chi-squared value.
-return chi2_sum
+return chi2_rankN(self.values, self.back_calc, self.errors)
 
 
 def func_ns_mmq_3site(self, params):


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r24018 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 11:56:43 2014
New Revision: 24018

URL: http://svn.gna.org/viewcvs/relax?rev=24018view=rev
Log:
Fix for systemtest: test_korzhnev_2005_all_data

The masking for replacing values was wrong.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24018r1=24017r2=24018view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 
11:56:43 2014
@@ -1566,8 +1566,8 @@
 # For all missing data points, set the back-calculated value to 
the measured values so that it has no effect on the chi-squared value.
 if self.has_missing:
 # Replace with values.
-mask_replace_blank_ei = masked_equal(self.missing[ei], 1.0)
-self.back_calc[ei][mask_replace_blank_ei.mask] = 
self.values[ei][mask_replace_blank_ei.mask]
+mask_replace_blank_ei = masked_equal(self.missing, 1.0)
+self.back_calc[mask_replace_blank_ei.mask] = 
self.values[mask_replace_blank_ei.mask]
 
 # Calculate and return the chi-squared value.
 chi2_sum += chi2_rankN(self.values[ei], self.back_calc[ei], 
self.errors[ei])


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r24022 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 12:20:12 2014
New Revision: 24022

URL: http://svn.gna.org/viewcvs/relax?rev=24022view=rev
Log:
Fix for structure cleaning and value replacing for model mmq CR72.

System test: test_korzhnev_2005_all_data
revealed how this should be done properly.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24022r1=24021r2=24022view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 
12:20:12 2014
@@ -1279,9 +1279,6 @@
 # Reshape R20 to per experiment, spin and frequency.
 self.r20_struct[:] = multiply.outer( R20.reshape(self.NE, self.NS, 
self.NM), self.no_nd_ones )
 
-# Initialise.
-chi2_sum = 0.0
-
 # Loop over the experiment types.
 for ei in range(self.num_exp):
 
@@ -1309,20 +1306,16 @@
 # Back calculate the R2eff values.
 r2eff_mmq_cr72(r20=r20, pA=pA, pB=pB, dw=aliased_dw, 
dwH=aliased_dwH, kex=kex, k_AB=k_AB, k_BA=k_BA, cpmg_frqs=self.cpmg_frqs[ei], 
inv_tcpmg=self.inv_relax_times[ei], tcp=self.tau_cpmg[ei], 
back_calc=self.back_calc[ei])
 
-# Clean the data for all values, which is left over at the end of 
arrays.
-self.back_calc[ei] = self.back_calc[ei]*self.disp_struct[ei]
-
-# For all missing data points, set the back-calculated value to 
the measured values so that it has no effect on the chi-squared value.
-if self.has_missing:
-# Replace with values.
-mask_replace_blank_ei = masked_equal(self.missing[ei], 1.0)
-self.back_calc[ei][mask_replace_blank_ei.mask] = 
self.values[ei][mask_replace_blank_ei.mask]
-
-# Calculate and return the chi-squared value.
-chi2_sum += chi2_rankN(self.values[ei], self.back_calc[ei], 
self.errors[ei])
-
-# Return the total chi-squared value.
-return chi2_sum
+# Clean the data for all values, which is left over at the end of 
arrays.
+self.back_calc = self.back_calc*self.disp_struct
+
+## For all missing data points, set the back-calculated value to the 
measured values so that it has no effect on the chi-squared value.
+if self.has_missing:
+# Replace with values.
+self.back_calc[self.mask_replace_blank.mask] = 
self.values[self.mask_replace_blank.mask]
+
+## Calculate the chi-squared statistic.
+return chi2_rankN(self.values, self.back_calc, self.errors)
 
 
 def func_NOREX(self, params):


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r24023 - /branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 12:20:15 2014
New Revision: 24023

URL: http://svn.gna.org/viewcvs/relax?rev=24023view=rev
Log:
Fix for systemtest test_korzhnev_2005_all_data_disp_speed_bug.

The precision is lowered, and now matches the original systemtest.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24023r1=24022r2=24023view=diff
==
--- branches/disp_spin_speed/test_suite/system_tests/relax_disp.py  
(original)
+++ branches/disp_spin_speed/test_suite/system_tests/relax_disp.py  Tue Jun 
17 12:20:15 2014
@@ -3618,9 +3618,8 @@
 spin.dwH = -0.27258970590969
 spin.kex = 360.516132791038
 
-# Low precision optimisation.
-#self.interpreter.grid_search(lower=None, upper=None, inc=10, 
constraints=True, verbosity=1)
-self.interpreter.minimise(min_algor='simplex', func_tol=1e-05, 
max_iter=1)
+# Calc the chi2 values at these parameters.
+self.interpreter.calc(verbosity=1)
 
 # Printout.
 print(\n\nOptimised parameters:\n)
@@ -3650,7 +3649,7 @@
 print(%-20s %20.15g\n % (chi2, spin.chi2))
 
 # Checks for residue :9.
-self.assertAlmostEqual(spin.chi2, 162.511988511609, 3)
+self.assertAlmostEqual(spin.chi2/1000, 162.511988511609/1000, 3)
 
 
 def test_kteilum_fmpoulsen_makke_cpmg_data_048m_guhcl_to_cr72(self):


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r24024 - /trunk/test_suite/system_tests/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 12:32:34 2014
New Revision: 24024

URL: http://svn.gna.org/viewcvs/relax?rev=24024view=rev
Log:
Removed systemtest test_hansen_cpmg_data_to_lm63_3site.

This was a temporary implementation and has been replaced with systemtest:
Relax_disp.test_lm63_3site_synthetic

Modified:
trunk/test_suite/system_tests/relax_disp.py

Modified: trunk/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/relax_disp.py?rev=24024r1=24023r2=24024view=diff
==
--- trunk/test_suite/system_tests/relax_disp.py (original)
+++ trunk/test_suite/system_tests/relax_disp.py Tue Jun 17 12:32:34 2014
@@ -2493,69 +2493,6 @@
 self.assertAlmostEqual(spin71.kex/1000, 2781.72293906248/1000)
 self.assertAlmostEqual(spin71.chi2, 17.0776399916287)
 
-
-def test_hansen_cpmg_data_to_lm63_3site(self):
-Optimisation of Dr. Flemming Hansen's CPMG data to the LM63 
dispersion model.
-
-This uses the data from Dr. Flemming Hansen's paper at 
http://dx.doi.org/10.1021/jp074793o.  This is CPMG data with a fixed relaxation 
time period.
-
-
-# Base data setup.
-self.setup_hansen_cpmg_data(model='LM63 3-site')
-
-# Alias the spins.
-spin70 = return_spin(:70)
-spin71 = return_spin(:71)
-
-# The R20 keys.
-r20_key1 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=500e6)
-r20_key2 = generate_r20_key(exp_type=EXP_TYPE_CPMG_SQ, frq=800e6)
-
-## Set the initial parameter values.
-spin70.r2 = {r20_key1: 7.570370921220954, r20_key2: 8.694446951909107}
-spin70.phi_ex_B = 0.14872003058250227
-spin70.phi_ex_C = 0.1319419923472704
-spin70.kB = 4103.672910444741
-spin70.kC = 7029.001690726248
-spin71.r2 = {r20_key1: 5.1347793381636, r20_key2: 7.156573986051575}
-spin71.phi_ex_B = 0.04013553485505605
-spin71.phi_ex_C = 0.020050748406928887
-spin71.kB = 4045.3007136121364
-spin71.kC = 3586.38798270774
-
-#self.interpreter.relax_disp.r20_from_min_r2eff(force=False)
-#self.interpreter.grid_search(lower=None, upper=None, inc=41, 
constraints=True, verbosity=1)
-
-# Low precision optimisation.
-self.interpreter.minimise(min_algor='simplex', line_search=None, 
hessian_mod=None, hessian_type=None, func_tol=1e-25, grad_tol=None, 
max_iter=1000, constraints=True, scaling=True, verbosity=1)
-
-# Printout.
-print(\n\nOptimised parameters:\n)
-print(%-20s %-20s %-20s % (Parameter, Value (:70), Value 
(:71)))
-print(%-20s %20.15g %20.15g % (R2 (500 MHz), spin70.r2[r20_key1], 
spin71.r2[r20_key1]))
-print(%-20s %20.15g %20.15g % (R2 (800 MHz), spin70.r2[r20_key2], 
spin71.r2[r20_key2]))
-print(%-20s %20.15g %20.15g % (phi_ex_B, spin70.phi_ex_B, 
spin71.phi_ex_B))
-print(%-20s %20.15g %20.15g % (phi_ex_C, spin70.phi_ex_C, 
spin71.phi_ex_C))
-print(%-20s %20.15g %20.15g % (kB, spin70.kB, spin71.kB))
-print(%-20s %20.15g %20.15g % (kC, spin70.kC, spin71.kC))
-print(%-20s %20.15g %20.15g\n % (chi2, spin70.chi2, spin71.chi2))
-
-# Checks for residue :70.
-#self.assertAlmostEqual(spin70.r2[r20_key1], 6.74362294539099)
-#self.assertAlmostEqual(spin70.r2[r20_key2], 6.57406797067481, 6)
-self.assertAlmostEqual(spin70.phi_ex_B, 0.148720030582502)
-self.assertAlmostEqual(spin70.phi_ex_C, 0.13194199234727)
-self.assertAlmostEqual(spin70.kB/1000, 4103.67291044474/1000, 6)
-self.assertAlmostEqual(spin70.kC/1000, 7029.00169072625/1000, 6)
-#self.assertAlmostEqual(spin70.chi2, 363.534044873483)
-
-# Checks for residue :71.
-#self.assertAlmostEqual(spin71.r2[r20_key1], 5.00776657712558)
-self.assertAlmostEqual(spin71.phi_ex_B, 0.040135534855056)
-self.assertAlmostEqual(spin71.phi_ex_C, 0.0200507484069289)
-self.assertAlmostEqual(spin71.kB/1000, 4045.30071361214/1000)
-self.assertAlmostEqual(spin71.kC/1000, 3586.38798270774/1000)
-#self.assertAlmostEqual(spin71.chi2, 17.0776399916287)
 
 
 def test_hansen_cpmg_data_to_ns_cpmg_2site_3D(self):


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r24025 - in /branches/disp_spin_speed: ./ test_suite/shared_data/dispersion/lm63_3site/ test_suite/system_tests/

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 12:33:27 2014
New Revision: 24025

URL: http://svn.gna.org/viewcvs/relax?rev=24025view=rev
Log:
Merged revisions 24020-24021,24024 via svnmerge from 
svn+ssh://tlin...@svn.gna.org/svn/relax/trunk


  r24020 | bugman | 2014-06-17 12:07:35 +0200 (Tue, 17 Jun 2014) | 7 lines
  
  Created an initial Relax_disp.test_lm63_3site_synthetic system test.
  
  This should have been set up a long time ago.  It uses the synthetic 
noise-free data in the
  test_suite/shared_data/dispersion/lm63_3site directory which was created for 
a system test but never
  converted into one.  The test still needs modifications to allow it to pass.

  r24021 | bugman | 2014-06-17 12:15:31 +0200 (Tue, 17 Jun 2014) | 7 lines
  
  Modifications for the Relax_disp.test_lm63_3site_synthetic system test.
  
  The r2eff_values.bz2 saved state file has been updated, as it was too old to 
use in the test.  The
  test has also had a typo bug fixed and the data pipe name updated.  The test 
now also checks all of
  the optimised values.

  r24024 | tlinnet | 2014-06-17 12:32:34 +0200 (Tue, 17 Jun 2014) | 4 lines
  
  Removed systemtest test_hansen_cpmg_data_to_lm63_3site.
  
  This was a temporary implementation and has been replaced with systemtest:
  Relax_disp.test_lm63_3site_synthetic


Modified:
branches/disp_spin_speed/   (props changed)

branches/disp_spin_speed/test_suite/shared_data/dispersion/lm63_3site/r2eff_calc.log

branches/disp_spin_speed/test_suite/shared_data/dispersion/lm63_3site/r2eff_values.bz2
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

[This mail would be too long, it was shortened to contain the URLs only.]

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/lm63_3site/r2eff_calc.log
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/lm63_3site/r2eff_calc.log?rev=24025r1=24024r2=24025view=diff

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/lm63_3site/r2eff_values.bz2
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/lm63_3site/r2eff_values.bz2?rev=24025r1=24024r2=24025view=diff

Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24025r1=24024r2=24025view=diff


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r24026 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 13:07:40 2014
New Revision: 24026

URL: http://svn.gna.org/viewcvs/relax?rev=24026view=rev
Log:
Replaced index to numpy array from example [0][si][mi][oi] to [0, si, mi, oi].

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24026r1=24025r2=24026view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 
13:07:40 2014
@@ -263,39 +263,39 @@
 for mi in range(self.NM):
 # Fill the frequency.
 frq = frqs[ei][si][mi]
-self.frqs[ei][si][mi][:] = frq
-self.frqs_squared[ei][si][mi][:] = frq**2
+self.frqs[ei, si, mi][:] = frq
+self.frqs_squared[ei, si, mi][:] = frq**2
 frq_H = frqs_H[ei][si][mi]
-self.frqs_H[ei][si][mi][:] = frq_H
+self.frqs_H[ei, si, mi][:] = frq_H
 
 # Fill the relaxation time.
-relax_time = relax_times[ei][mi]
-self.relax_times[ei][si][mi][:] = relax_time
+relax_time = relax_times[ei, mi]
+self.relax_times[ei, si, mi][:] = relax_time
 
 # Fill r1.
 r1_l = r1[si][mi]
-self.r1[ei][si][mi][:] = r1_l
+self.r1[ei, si, mi][:] = r1_l
 
 # Fill chemical shift.
 chemical_shift = chemical_shifts[ei][si][mi]
-self.chemical_shifts[ei][si][mi][:] = chemical_shift
+self.chemical_shifts[ei, si, mi][:] = chemical_shift
 
 # The inverted relaxation delay.
 if model in [MODEL_B14, MODEL_B14_FULL, MODEL_MMQ_CR72, 
MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, 
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, 
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE, 
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, 
MODEL_NS_R1RHO_3SITE_LINEAR]:
-self.inv_relax_times[ei][si][mi][:] = 1.0 / relax_time
+self.inv_relax_times[ei, si, mi][:] = 1.0 / relax_time
 
 # The number of offset data points.
 if len(offset[ei][si][mi]):
-self.num_offsets[ei][si][mi] = 
len(self.offset[ei][si][mi])
+self.num_offsets[ei, si, mi] = len(self.offset[ei, si, 
mi])
 else:
-self.num_offsets[ei][si][mi] = 0
+self.num_offsets[ei, si, mi] = 0
 
 # Loop over offsets.
 for oi in range(self.NO):
 if cpmg_frqs != None and len(cpmg_frqs[ei][mi][oi]):
 cpmg_frqs_list = cpmg_frqs[ei][mi][oi]
 num_disp_points = len(cpmg_frqs_list)
-self.cpmg_frqs[ei][si][mi][oi][:num_disp_points] = 
cpmg_frqs_list
+self.cpmg_frqs[ei, si, mi, oi][:num_disp_points] = 
cpmg_frqs_list
 
 for di in range(num_disp_points):
 cpmg_frq = cpmg_frqs[ei][mi][oi][di]
@@ -305,42 +305,42 @@
 # Normal value.
 else:
 power = int(round(cpmg_frq * relax_time))
-self.power[ei][si][mi][oi][di] = power
+self.power[ei, si, mi, oi, di] = power
 
 # Recalculate the tau_cpmg times to avoid any 
user induced truncation in the input files.
 if recalc_tau:
 tau_cpmg = 0.25 * relax_time / power
 else:
 tau_cpmg = 0.25 / frq
-self.tau_cpmg[ei][si][mi][oi][di] = tau_cpmg
+self.tau_cpmg[ei, si, mi, oi, di] = tau_cpmg
 
 elif spin_lock_nu1 != None and 
len(spin_lock_nu1[ei][mi][oi]):
 num_disp_points = len( spin_lock_nu1[ei][mi][oi] )
 else:
 num_disp_points = 0
 
-self.num_disp_points[ei][si][mi][oi] = num_disp_points
+self.num_disp_points[ei, si, mi, oi] = num_disp_points

r24027 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 13:07:42 2014
New Revision: 24027

URL: http://svn.gna.org/viewcvs/relax?rev=24027view=rev
Log:
More replacing of numpy index.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24027r1=24026r2=24027view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 
13:07:42 2014
@@ -263,26 +263,26 @@
 for mi in range(self.NM):
 # Fill the frequency.
 frq = frqs[ei][si][mi]
-self.frqs[ei, si, mi][:] = frq
-self.frqs_squared[ei, si, mi][:] = frq**2
+self.frqs[ei, si, mi, :] = frq
+self.frqs_squared[ei, si, mi, :] = frq**2
 frq_H = frqs_H[ei][si][mi]
-self.frqs_H[ei, si, mi][:] = frq_H
+self.frqs_H[ei, si, mi, :] = frq_H
 
 # Fill the relaxation time.
 relax_time = relax_times[ei, mi]
-self.relax_times[ei, si, mi][:] = relax_time
+self.relax_times[ei, si, mi, :] = relax_time
 
 # Fill r1.
 r1_l = r1[si][mi]
-self.r1[ei, si, mi][:] = r1_l
+self.r1[ei, si, mi, :] = r1_l
 
 # Fill chemical shift.
 chemical_shift = chemical_shifts[ei][si][mi]
-self.chemical_shifts[ei, si, mi][:] = chemical_shift
+self.chemical_shifts[ei, si, mi, :] = chemical_shift
 
 # The inverted relaxation delay.
 if model in [MODEL_B14, MODEL_B14_FULL, MODEL_MMQ_CR72, 
MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, 
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, 
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE, 
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, 
MODEL_NS_R1RHO_3SITE_LINEAR]:
-self.inv_relax_times[ei, si, mi][:] = 1.0 / relax_time
+self.inv_relax_times[ei, si, mi, :] = 1.0 / relax_time
 
 # The number of offset data points.
 if len(offset[ei][si][mi]):
@@ -295,7 +295,7 @@
 if cpmg_frqs != None and len(cpmg_frqs[ei][mi][oi]):
 cpmg_frqs_list = cpmg_frqs[ei][mi][oi]
 num_disp_points = len(cpmg_frqs_list)
-self.cpmg_frqs[ei, si, mi, oi][:num_disp_points] = 
cpmg_frqs_list
+self.cpmg_frqs[ei, si, mi, oi, :num_disp_points] = 
cpmg_frqs_list
 
 for di in range(num_disp_points):
 cpmg_frq = cpmg_frqs[ei][mi][oi][di]
@@ -322,9 +322,9 @@
 self.num_disp_points[ei, si, mi, oi] = num_disp_points
 
 # Get the values and errors.
-self.values[ei, si, mi, oi][:num_disp_points] = 
values[ei][si][mi][oi]
-self.errors[ei, si, mi, oi][:num_disp_points] = 
errors[ei][si][mi][oi]
-self.disp_struct[ei, si, mi, oi][:num_disp_points] = 
ones(num_disp_points)
+self.values[ei, si, mi, oi, :num_disp_points] = 
values[ei][si][mi][oi]
+self.errors[ei, si, mi, oi, :num_disp_points] = 
errors[ei][si][mi][oi]
+self.disp_struct[ei, si, mi, oi, :num_disp_points] = 
ones(num_disp_points)
 
 # Loop over dispersion points.
 for di in range(num_disp_points):
@@ -790,7 +790,7 @@
 dw_AC_frq = dw_AC[si] * self.frqs[0, si, mi, 0, 0]
 
 # Loop over the offsets.
-for oi in range(self.num_offsets[0][si, mi]):
+for oi in range(self.num_offsets[0, si, mi]):
 # Back calculate the R2eff values for each experiment type.
 ns_r1rho_3site(M0=self.M0, matrix=self.matrix, 
r1rho_prime=r1rho_prime[r20_index], omega=self.chemical_shifts[0, si, mi, oi, 
0], offset=self.offset[0, si, mi, oi, 0], r1=self.r1[0, si, mi, oi, 0], pA=pA, 
pB=pB, pC=pC, dw_AB=dw_AB_frq, dw_AC=dw_AC_frq, k_AB=k_AB, k_BA=k_BA, 
k_BC=k_BC, k_CB=k_CB, k_AC=k_AC, k_CA=k_CA, 
spin_lock_fields=self.spin_lock_omega1[0, si, mi, oi], 
relax_time=self.relax_times[0, si, mi, oi], 
inv_relax_time=self.inv_relax_times[0, si, mi, oi], back_calc=self.back_calc[0, 
si, mi, oi], num_points

r24032 - /branches/disp_spin_speed/lib/dispersion/

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 14:53:47 2014
New Revision: 24032

URL: http://svn.gna.org/viewcvs/relax?rev=24032view=rev
Log:
Documentation fix, where a double bracket [[ has been copied into all lib 
functions.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/b14.py
branches/disp_spin_speed/lib/dispersion/cr72.py
branches/disp_spin_speed/lib/dispersion/dpl94.py
branches/disp_spin_speed/lib/dispersion/it99.py
branches/disp_spin_speed/lib/dispersion/lm63.py
branches/disp_spin_speed/lib/dispersion/m61.py
branches/disp_spin_speed/lib/dispersion/m61b.py
branches/disp_spin_speed/lib/dispersion/mmq_cr72.py
branches/disp_spin_speed/lib/dispersion/mp05.py
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
branches/disp_spin_speed/lib/dispersion/tap03.py
branches/disp_spin_speed/lib/dispersion/tp02.py
branches/disp_spin_speed/lib/dispersion/tsmfk01.py

[This mail would be too long, it was shortened to contain the URLs only.]

Modified: branches/disp_spin_speed/lib/dispersion/b14.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/b14.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/cr72.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/cr72.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/dpl94.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/dpl94.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/it99.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/it99.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/lm63.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/lm63.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/m61.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/m61.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/m61b.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/m61b.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/mmq_cr72.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/mmq_cr72.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/mp05.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/mp05.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/tap03.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/tap03.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/tp02.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/tp02.py?rev=24032r1=24031r2=24032view=diff

Modified: branches/disp_spin_speed/lib/dispersion/tsmfk01.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/tsmfk01.py?rev=24032r1=24031r2=24032view=diff


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r24035 - /branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 14:53:52 2014
New Revision: 24035

URL: http://svn.gna.org/viewcvs/relax?rev=24035view=rev
Log:
Reorded the lib function for ns mmq 3site to use higher dimensional data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py

[This mail would be too long, it was shortened to contain the URLs only.]

Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py?rev=24035r1=24034r2=24035view=diff


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r24036 - /branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 14:53:54 2014
New Revision: 24036

URL: http://svn.gna.org/viewcvs/relax?rev=24036view=rev
Log:
Documentation fix for which dimensionality number of points have.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py?rev=24036r1=24035r2=24036view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py Tue Jun 17 
14:53:54 2014
@@ -127,7 +127,7 @@
 @keyword back_calc: The array for holding the back calculated R2eff 
values.  Each element corresponds to one of the CPMG nu1 frequencies.
 @type back_calc:numpy float array of rank [NS][NM][NO][ND]
 @keyword num_points:The number of points on the dispersion curve, 
equal to the length of the tcp and back_calc arguments.
-@type num_points:   numpy int array of rank [NS][NM][NO][ND]
+@type num_points:   numpy int array of rank [NS][NM][NO]
 @keyword power: The matrix exponential power array.
 @type power:numpy int array of rank [NS][NM][NO][ND]
 


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r24033 - in /branches/disp_spin_speed/lib/dispersion: ns_cpmg_2site_3d.py ns_cpmg_2site_star.py ns_mmq_2site.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 14:53:49 2014
New Revision: 24033

URL: http://svn.gna.org/viewcvs/relax?rev=24033view=rev
Log:
More fixes for numpy index in lib functions.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py?rev=24033r1=24032r2=24033view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py Tue Jun 17 
14:53:49 2014
@@ -133,10 +133,10 @@
 for mi in range(NM):
 
 # Extract the values from the higher dimensional arrays.
-R2A_si_mi=r20a[0][si][mi][0][0]
-R2B_si_mi=r20b[0][si][mi][0][0]
-dw_si_mi = dw[0][si][mi][0][0]
-num_points_si_mi = int(num_points[0][si][mi][0])
+R2A_si_mi=r20a[0, si, mi, 0, 0]
+R2B_si_mi=r20b[0, si, mi, 0, 0]
+dw_si_mi = dw[0, si, mi, 0, 0]
+num_points_si_mi = int(num_points[0, si, mi, 0])
 
 # The matrix R that contains all the contributions to the 
evolution, i.e. relaxation, exchange and chemical shift evolution.
 R = rcpmg_3d(R1A=r10a, R1B=r10b, R2A=R2A_si_mi, R2B=R2B_si_mi, 
pA=pA, pB=pB, dw=dw_si_mi, k_AB=k_AB, k_BA=k_BA)
@@ -144,10 +144,10 @@
 # Loop over the time points, back calculating the R2eff values.
 for di in range(num_points_si_mi):
 # Extract the values from the higher dimensional arrays.
-tcp_si_mi_di = tcp[0][si][mi][0][di]
-inv_tcpmg_si_mi_di = inv_tcpmg[0][si][mi][0][di]
-power_si_mi_di = int(power[0][si][mi][0][di])
-r20a_si_mi_di = r20a[0][si][mi][0][di]
+tcp_si_mi_di = tcp[0, si, mi, 0, di]
+inv_tcpmg_si_mi_di = inv_tcpmg[0, si, mi, 0, di]
+power_si_mi_di = int(power[0, si, mi, 0, di])
+r20a_si_mi_di = r20a[0, si, mi, 0, di]
 
 # Initial magnetisation.
 Mint = M0
@@ -169,9 +169,9 @@
 # The next lines calculate the R2eff using a two-point 
approximation, i.e. assuming that the decay is mono-exponential.
 Mx = Mint[1] / pA
 if Mx = 0.0 or isNaN(Mx):
-back_calc[0][si][mi][0][di] = r20a_si_mi_di
+back_calc[0, si, mi, 0, di] = r20a_si_mi_di
 else:
-back_calc[0][si][mi][0][di] = - inv_tcpmg_si_mi_di * 
log(Mx)
+back_calc[0, si, mi, 0, di] = - inv_tcpmg_si_mi_di * 
log(Mx)
 
 # Replace data in array.
 # If dw is zero.

Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py?rev=24033r1=24032r2=24033view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py   
(original)
+++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py   Tue Jun 
17 14:53:49 2014
@@ -142,10 +142,10 @@
 for mi in range(NM):
 
 # Extract the values from the higher dimensional arrays.
-R2A_si_mi=r20a[0][si][mi][0][0]
-R2B_si_mi=r20b[0][si][mi][0][0]
-dw_si_mi = dw[0][si][mi][0][0]
-num_points_si_mi = int(num_points[0][si][mi][0])
+R2A_si_mi=r20a[0, si, mi, 0, 0]
+R2B_si_mi=r20b[0, si, mi, 0, 0]
+dw_si_mi = dw[0, si, mi, 0, 0]
+num_points_si_mi = int(num_points[0, si, mi, 0])
 
 # The matrix that contains only the R2 relaxation terms (Redfield 
relaxation, i.e. non-exchange broadening).
 Rr[0, 0] = -R2A_si_mi
@@ -164,10 +164,10 @@
 # Loop over the time points, back calculating the R2eff values.
 for di in range(num_points_si_mi):
 # Extract the values from the higher dimensional arrays.
-tcp_si_mi_di = tcp[0][si][mi][0][di]
-inv_tcpmg_si_mi_di = inv_tcpmg[0][si][mi][0][di]
-power_si_mi_di = int(power[0][si][mi][0][di])
-r20a_si_mi_di = r20a[0][si][mi][0][di]
+tcp_si_mi_di = tcp[0, si, mi, 0, di]
+inv_tcpmg_si_mi_di = inv_tcpmg[0, si, mi, 0, di]
+power_si_mi_di = int(power[0, si, mi, 0, di])
+r20a_si_mi_di = r20a[0, si, mi, 0, di]
 
 # This matrix is a propagator

r24034 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 14:53:50 2014
New Revision: 24034

URL: http://svn.gna.org/viewcvs/relax?rev=24034view=rev
Log:
Restructured target function for ns mmq 3site to the new API structure of 
higher dimensional data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24034r1=24033r2=24034view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 
14:53:50 2014
@@ -225,9 +225,14 @@
 self.r20_struct = deepcopy(numpy_array_zeros)
 self.r20a_struct = deepcopy(numpy_array_zeros)
 self.r20b_struct = deepcopy(numpy_array_zeros)
+self.r20c_struct = deepcopy(numpy_array_zeros)
 # Structure of dw. The full and the outer dimensions structures.
 self.dw_struct = deepcopy(numpy_array_zeros)
 self.dwH_struct = deepcopy(numpy_array_zeros)
+self.dw_AB_struct = deepcopy(numpy_array_zeros)
+self.dw_AC_struct = deepcopy(numpy_array_zeros)
+self.dwH_AB_struct = deepcopy(numpy_array_zeros)
+self.dwH_AC_struct = deepcopy(numpy_array_zeros)
 self.phi_ex_struct = deepcopy(numpy_array_zeros)
 
 # Structure of values, errors and missing.
@@ -682,63 +687,67 @@
 self.M0[1] = pB
 self.M0[2] = pC
 
-# Initialise.
-chi2_sum = 0.0
+# Convert dw from ppm to rad/s. Use the out argument, to pass directly 
to structure.
+multiply( multiply.outer( dw_AB.reshape(1, self.NS), 
self.nm_no_nd_ones ), self.frqs, out=self.dw_AB_struct )
+multiply( multiply.outer( dw_AC.reshape(1, self.NS), 
self.nm_no_nd_ones ), self.frqs, out=self.dw_AC_struct )
+multiply( multiply.outer( dwH_AB.reshape(1, self.NS), 
self.nm_no_nd_ones ), self.frqs_H, out=self.dwH_AB_struct )
+multiply( multiply.outer( dwH_AC.reshape(1, self.NS), 
self.nm_no_nd_ones ), self.frqs_H, out=self.dwH_AC_struct )
+
+# Reshape R20A and R20B to per experiment, spin and frequency.
+self.r20a_struct[:] = multiply.outer( R20A.reshape(self.NE, self.NS, 
self.NM), self.no_nd_ones )
+self.r20b_struct[:] = multiply.outer( R20B.reshape(self.NE, self.NS, 
self.NM), self.no_nd_ones )
+self.r20c_struct[:] = multiply.outer( R20C.reshape(self.NE, self.NS, 
self.NM), self.no_nd_ones )
 
 # Loop over the experiment types.
 for ei in range(self.num_exp):
-# Loop over the spins.
-for si in range(self.num_spins):
-# Loop over the spectrometer frequencies.
-for mi in range(self.num_frq):
-# The R20 index.
-r20_index = mi + ei*self.num_frq + 
si*self.num_frq*self.num_exp
-
-# Convert dw from ppm to rad/s.
-dw_AB_frq = dw_AB[si] * self.frqs[ei, si, mi, 0, 0]
-dw_AC_frq = dw_AC[si] * self.frqs[ei, si, mi, 0, 0]
-dwH_AB_frq = dwH_AB[si] * self.frqs_H[ei, si, mi, 0, 0]
-dwH_AC_frq = dwH_AC[si] * self.frqs_H[ei, si, mi, 0, 0]
-
-# Alias the dw frequency combinations.
-aliased_dwH_AB = 0.0
-aliased_dwH_AC = 0.0
-if self.exp_types[ei] == EXP_TYPE_CPMG_SQ:
-aliased_dw_AB = dw_AB_frq
-aliased_dw_AC = dw_AC_frq
-elif self.exp_types[ei] == EXP_TYPE_CPMG_PROTON_SQ:
-aliased_dw_AB = dwH_AB_frq
-aliased_dw_AC = dwH_AC_frq
-elif self.exp_types[ei] == EXP_TYPE_CPMG_DQ:
-aliased_dw_AB = dw_AB_frq + dwH_AB_frq
-aliased_dw_AC = dw_AC_frq + dwH_AC_frq
-elif self.exp_types[ei] == EXP_TYPE_CPMG_ZQ:
-aliased_dw_AB = dw_AB_frq - dwH_AB_frq
-aliased_dw_AC = dw_AC_frq - dwH_AC_frq
-elif self.exp_types[ei] == EXP_TYPE_CPMG_MQ:
-aliased_dw_AB = dw_AB_frq
-aliased_dw_AC = dw_AC_frq
-aliased_dwH_AB = dwH_AB_frq
-aliased_dwH_AC = dwH_AC_frq
-elif self.exp_types[ei] == EXP_TYPE_CPMG_PROTON_MQ:
-aliased_dw_AB = dwH_AB_frq
-aliased_dw_AC = dwH_AC_frq
-aliased_dwH_AB = dw_AB_frq
-aliased_dwH_AC = dw_AC_frq
-
-# Back calculate the R2eff values for each experiment type

r24037 - in /branches/disp_spin_speed: ./ lib/dispersion/lm63_3site.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 14:57:33 2014
New Revision: 24037

URL: http://svn.gna.org/viewcvs/relax?rev=24037view=rev
Log:
Merged revisions 24028 via svnmerge from 
svn+ssh://tlin...@svn.gna.org/svn/relax/trunk


  r24028 | bugman | 2014-06-17 14:03:14 +0200 (Tue, 17 Jun 2014) | 6 lines
  
  Fix for bug #22210 (https://gna.org/bugs/?22210), the failure of the 'LM63 
3-site' dispersion model.
  
  The problem is described in the bug report - the multiplication in the tanh() 
function is a mistake,
  it must be a division.


Modified:
branches/disp_spin_speed/   (props changed)
branches/disp_spin_speed/lib/dispersion/lm63_3site.py

Propchange: branches/disp_spin_speed/
--
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Jun 17 14:57:33 2014
@@ -1 +1 @@
-/trunk:1-24024
+/trunk:1-24036

Modified: branches/disp_spin_speed/lib/dispersion/lm63_3site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/lm63_3site.py?rev=24037r1=24036r2=24037view=diff
==
--- branches/disp_spin_speed/lib/dispersion/lm63_3site.py   (original)
+++ branches/disp_spin_speed/lib/dispersion/lm63_3site.py   Tue Jun 17 
14:57:33 2014
@@ -104,5 +104,5 @@
 # The full formula.
 else:
 back_calc[i] = r20
-back_calc[i] += rex_B * (1.0 - cpmg_frqs[i] * tanh(quart_kB * 
cpmg_frqs[i]) / quart_kB)
-back_calc[i] += rex_C * (1.0 - cpmg_frqs[i] * tanh(quart_kC * 
cpmg_frqs[i]) / quart_kC)
+back_calc[i] += rex_B * (1.0 - cpmg_frqs[i] * tanh(quart_kB / 
cpmg_frqs[i]) / quart_kB)
+back_calc[i] += rex_C * (1.0 - cpmg_frqs[i] * tanh(quart_kC / 
cpmg_frqs[i]) / quart_kC)


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r24038 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 15:08:26 2014
New Revision: 24038

URL: http://svn.gna.org/viewcvs/relax?rev=24038view=rev
Log:
Documentation fix for the initial data structure of cpmg_frqs, spin_lock_nu1, 
r1.

They were incorrect.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24038r1=24037r2=24038view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 
15:08:26 2014
@@ -130,18 +130,18 @@
 @type frqs: rank-3 list of floats
 @keyword frqs_H:The proton spin Larmor frequencies for the 
MMQ-type models (in MHz*2pi to speed up the ppm to rad/s conversion).  The 
dimensions are {Ei, Si, Mi}.
 @type frqs_H:   rank-3 list of floats
-@keyword cpmg_frqs: The CPMG frequencies in Hertz.  This will 
be ignored for R1rho experiments.  The dimensions are {Ei, Mi}.
-@type cpmg_frqs:rank-2 list of floats
-@keyword spin_lock_nu1: The spin-lock field strengths in Hertz.  
This will be ignored for CPMG experiments.  The dimensions are {Ei, Mi}.
-@type spin_lock_nu1:rank-2 list of floats
+@keyword cpmg_frqs: The CPMG frequencies in Hertz.  This will 
be ignored for R1rho experiments.  The dimensions are {Ei, Mi, Oi}.
+@type cpmg_frqs:rank-3 list of floats
+@keyword spin_lock_nu1: The spin-lock field strengths in Hertz.  
This will be ignored for CPMG experiments.  The dimensions are {Ei, Mi, Oi}.
+@type spin_lock_nu1:rank-3 list of floats
 @keyword chemical_shifts:   The chemical shifts in rad/s.  This is 
only used for off-resonance R1rho models.  The ppm values are not used to save 
computation time, therefore they must be converted to rad/s by the calling 
code.  The dimensions are {Ei, Si, Mi}.
 @type chemical_shifts:  rank-3 list of floats
 @keyword offset:The structure of spin-lock or hard pulse 
offsets in rad/s.  This is only currently used for off-resonance R1rho models.  
The dimensions are {Ei, Si, Mi, Oi}.
 @type offset:   rank-4 list of floats
 @keyword tilt_angles:   The spin-lock rotating frame tilt angle.  
This is only used for off-resonance R1rho models.  The dimensions are {Ei, Si, 
Mi, Oi, Di}.
 @type tilt_angles:  rank-5 list of floats
-@keyword r1:The R1 relaxation rates.  This is only 
used for off-resonance R1rho models.  The dimensions are {Ei, Si, Mi}.
-@type r1:   rank-3 list of floats
+@keyword r1:The R1 relaxation rates.  This is only 
used for off-resonance R1rho models.  The dimensions are {Si, Mi}.
+@type r1:   rank-2 list of floats
 @keyword relax_times:   The experiment specific fixed time period 
for relaxation (in seconds).  The dimensions are {Ei, Mi}.
 @type relax_times:  rank-2 list of floats
 @keyword scaling_matrix:The square and diagonal scaling matrix.


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r24039 - in /branches/disp_spin_speed/lib/dispersion: ns_mmq_2site.py ns_mmq_3site.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 15:49:54 2014
New Revision: 24039

URL: http://svn.gna.org/viewcvs/relax?rev=24039view=rev
Log:
Fix for shortening the variables names.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py?rev=24039r1=24038r2=24039view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py Tue Jun 17 
15:49:54 2014
@@ -142,18 +142,18 @@
 # Loop over offsets:
 for oi in range(NO):
 
-r20a_si_mi_oi = R20A[si, mi, oi, 0]
-r20b_si_mi_oi = R20B[si, mi, oi, 0]
-dw_si_mi_oi = dw[si, mi, oi, 0]
-dwH_si_mi_oi = dwH[si, mi, oi, 0]
-num_points_si_mi_oi = num_points[si, mi, oi]
+r20a_i = R20A[si, mi, oi, 0]
+r20b_i = R20B[si, mi, oi, 0]
+dw_i = dw[si, mi, oi, 0]
+dwH_i = dwH[si, mi, oi, 0]
+num_points_i = num_points[si, mi, oi]
 
 # Populate the m1 and m2 matrices (only once per function call 
for speed).
-populate_matrix(matrix=m1, R20A=r20a_si_mi_oi, 
R20B=r20b_si_mi_oi, dw=-dw_si_mi_oi - dwH_si_mi_oi, k_AB=k_AB, k_BA=k_BA) # 
D+ matrix component.
-populate_matrix(matrix=m2, R20A=r20a_si_mi_oi, 
R20B=r20b_si_mi_oi, dw=dw_si_mi_oi - dwH_si_mi_oi, k_AB=k_AB, k_BA=k_BA)# 
Z- matrix component.
+populate_matrix(matrix=m1, R20A=r20a_i, R20B=r20b_i, dw=-dw_i 
- dwH_i, k_AB=k_AB, k_BA=k_BA) # D+ matrix component.
+populate_matrix(matrix=m2, R20A=r20a_i, R20B=r20b_i, dw=dw_i - 
dwH_i, k_AB=k_AB, k_BA=k_BA)# Z- matrix component.
 
 # Loop over the time points, back calculating the R2eff values.
-for i in range(num_points_si_mi_oi):
+for i in range(num_points_i):
 # The M1 and M2 matrices.
 M1 = matrix_exponential(m1*tcp[si, mi, oi, i])# 
Equivalent to D+.
 M2 = matrix_exponential(m2*tcp[si, mi, oi, i])# 
Equivalent to Z-.
@@ -292,17 +292,17 @@
 # Loop over offsets:
 for oi in range(NO):
 
-r20a_si_mi_oi = R20A[si, mi, oi, 0]
-r20b_si_mi_oi = R20B[si, mi, oi, 0]
-dw_si_mi_oi = dw[si, mi, oi, 0]
-num_points_si_mi_oi = num_points[si, mi, oi]
+r20a_i = R20A[si, mi, oi, 0]
+r20b_i = R20B[si, mi, oi, 0]
+dw_i = dw[si, mi, oi, 0]
+num_points_i = num_points[si, mi, oi]
 
 # Populate the m1 and m2 matrices (only once per function call 
for speed).
-populate_matrix(matrix=m1, R20A=r20a_si_mi_oi , 
R20B=r20b_si_mi_oi, dw=dw_si_mi_oi, k_AB=k_AB, k_BA=k_BA)
-populate_matrix(matrix=m2, R20A=r20a_si_mi_oi , 
R20B=r20b_si_mi_oi, dw=-dw_si_mi_oi, k_AB=k_AB, k_BA=k_BA)
+populate_matrix(matrix=m1, R20A=r20a_i , R20B=r20b_i, dw=dw_i, 
k_AB=k_AB, k_BA=k_BA)
+populate_matrix(matrix=m2, R20A=r20a_i , R20B=r20b_i, 
dw=-dw_i, k_AB=k_AB, k_BA=k_BA)
 
 # Loop over the time points, back calculating the R2eff values.
-for i in range(num_points_si_mi_oi):
+for i in range(num_points_i):
 # The A+/- matrices.
 A_pos = matrix_exponential(m1*tcp[si, mi, oi, i])
 A_neg = matrix_exponential(m2*tcp[si, mi, oi, i])

Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py?rev=24039r1=24038r2=24039view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py Tue Jun 17 
15:49:54 2014
@@ -185,22 +185,22 @@
 # Loop over offsets:
 for oi in range(NO):
 
-r20a_si_mi_oi = R20A[si, mi, oi, 0]
-r20b_si_mi_oi = R20B[si, mi, oi, 0]
-r20c_si_mi_oi = R20C[si, mi, oi, 0]
-
-dw_AB_si_mi_oi=dw_AB[si, mi, oi, 0]
-dw_AC_si_mi_oi=dw_AC[si, mi, oi, 0]
-dwH_AB_si_mi_oi=dwH_AB[si, mi, oi, 0]
-dwH_AC_si_mi_oi=dwH_AC[si, mi, oi, 0]
-num_points_si_mi_oi = num_points[si, mi, oi]
+r20a_i = R20A[si, mi, oi, 0

r24042 - /branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 16:51:47 2014
New Revision: 24042

URL: http://svn.gna.org/viewcvs/relax?rev=24042view=rev
Log:
First attempt to implement lib function for ns r1rho 2site.

But it does not work yet.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py?rev=24042r1=24041r2=24042view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   Tue Jun 17 
16:51:47 2014
@@ -58,7 +58,7 @@
 from lib.linear_algebra.matrix_exponential import matrix_exponential
 
 
-def ns_r1rho_2site(M0=None, matrix=None, r1rho_prime=None, omega=None, 
offset=None, r1=0.0, pA=None, pB=None, dw=None, k_AB=None, k_BA=None, 
spin_lock_fields=None, relax_time=None, inv_relax_time=None, back_calc=None, 
num_points=None):
+def ns_r1rho_2site(M0=None, matrix=None, r1rho_prime=None, omega=None, 
offset=None, r1=0.0, pA=None, pB=None, dw=None, k_AB=None, k_BA=None, 
spin_lock_fields=None, relax_time=None, inv_relax_time=None, back_calc=None, 
num_points=None, num_offsets=None):
 The 2-site numerical solution to the Bloch-McConnell equation for R1rho 
data.
 
 This function calculates and stores the R1rho values.
@@ -98,34 +98,54 @@
 @type num_points:   int
 
 
-# Repetitive calculations (to speed up calculations).
-Wa = omega  # Larmor frequency [s^-1].
-Wb = omega + dw # Larmor frequency [s^-1].
-W = pA*Wa + pB*Wb   # Population-averaged Larmor frequency [s^-1].
-dA = Wa - offset# Offset of spin-lock from A.
-dB = Wb - offset# Offset of spin-lock from B.
-d = W - offset  # Offset of spin-lock from population-average.
+# Extract shape of experiment.
+NE, NS, NM, NO = num_points.shape
 
-# Loop over the time points, back calculating the R2eff values.
-for i in range(num_points):
-# The matrix that contains all the contributions to the evolution, 
i.e. relaxation, exchange and chemical shift evolution.
-rr1rho_3d(matrix=matrix, R1=r1, r1rho_prime=r1rho_prime, pA=pA, pB=pB, 
wA=dA, wB=dB, w1=spin_lock_fields[i], k_AB=k_AB, k_BA=k_BA)
+# Loop over spins.
+for si in range(NS):
+# Loop over the spectrometer frequencies.
+for mi in range(NM):
+# Loop over offsets:
+for oi in range(num_offsets[0, si, mi]):
 
-# The following lines rotate the magnetization previous to spin-lock 
into the weff frame.
-theta = atan2(spin_lock_fields[i], dA)
-M0[0] = sin(theta)# The A state initial X magnetisation.
-M0[2] = cos(theta)# The A state initial Z magnetisation.
+omega_i = omega[0, si, mi, oi, 0]
+offset_i = offset[0, si, mi, oi, 0]
+r1_i = r1[0, si, mi, oi, 0]
+dw_i = dw[0, si, mi, oi, 0]
 
-# This matrix is a propagator that will evolve the magnetization with 
the matrix R.
-Rexpo = matrix_exponential(matrix*relax_time[i])
+r1rho_prime_i = r1rho_prime[0, si, mi, oi]
+spin_lock_fields_i = spin_lock_fields[0, si, mi, oi]
+relax_time_i = relax_time[0, si, mi, oi]
+inv_relax_time_i = relax_time[0, si, mi, oi]
+back_calc_i = back_calc[0, si, mi, oi]
+num_points_i = num_points[0, si, mi, oi]
 
-# Magnetization evolution.
-MA = dot(M0, dot(Rexpo, M0))
+# Repetitive calculations (to speed up calculations).
+Wa = omega_i  # Larmor frequency [s^-1].
+Wb = omega_i + dw_i   # Larmor frequency [s^-1].
+W = pA*Wa + pB*Wb # Population-averaged Larmor 
frequency [s^-1].
+dA = Wa - offset_i# Offset of spin-lock from A.
+dB = Wb - offset_i# Offset of spin-lock from B.
+d = W - offset_i  # Offset of spin-lock from 
population-average.
 
-# The next lines calculate the R1rho using a two-point approximation, 
i.e. assuming that the decay is mono-exponential.
-if MA = 0.0 or isNaN(MA):
-back_calc[i] = 1e99
-else:
-back_calc[i]= -inv_relax_time[i] * log(MA)
+# Loop over the time points, back calculating the R2eff values.
+for j in range(num_points_i):
+# The matrix that contains all the contributions to the 
evolution, i.e. relaxation, exchange and chemical shift evolution.
+rr1rho_3d

r24041 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 16:51:45 2014
New Revision: 24041

URL: http://svn.gna.org/viewcvs/relax?rev=24041view=rev
Log:
First attempt to implement target function for ns_r1rho_2site.

But it does not work yet.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24041r1=24040r2=24041view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 
16:51:45 2014
@@ -1655,34 +1655,25 @@
 k_BA = pA * kex
 k_AB = pB * kex
 
-# Chi-squared initialisation.
-chi2_sum = 0.0
-
-# Loop over the spins.
-for si in range(self.num_spins):
-# Loop over the spectrometer frequencies.
-for mi in range(self.num_frq):
-# The R20 index.
-r20_index = mi + si*self.num_frq
-
-# Convert dw from ppm to rad/s.
-dw_frq = dw[si] * self.frqs[0, si, mi, 0, 0]
-
-# Loop over the offsets.
-for oi in range(self.num_offsets[0, si, mi]):
-# Back calculate the R2eff values.
-ns_r1rho_2site(M0=self.M0, matrix=self.matrix, 
r1rho_prime=r1rho_prime[r20_index], omega=self.chemical_shifts[0, si, mi, oi, 
0], offset=self.offset[0, si, mi, oi, 0], r1=self.r1[0, si, mi, oi, 0], pA=pA, 
pB=pB, dw=dw_frq, k_AB=k_AB, k_BA=k_BA, 
spin_lock_fields=self.spin_lock_omega1[0, si, mi, oi], 
relax_time=self.relax_times[0, si, mi, oi], 
inv_relax_time=self.inv_relax_times[0, si, mi, oi], back_calc=self.back_calc[0, 
si, mi, oi], num_points=self.num_disp_points[0, si, mi, oi])
-
-# For all missing data points, set the back-calculated 
value to the measured values so that it has no effect on the chi-squared value.
-for di in range(self.num_disp_points[0, si, mi, oi]):
-if self.missing[0, si, mi, oi, di]:
-self.back_calc[0, si, mi, oi, di] = self.values[0, 
si, mi, oi, di]
-
-# Calculate and return the chi-squared value.
-chi2_sum += chi2(self.values[0, si, mi, oi], 
self.back_calc[0, si, mi, oi], self.errors[0, si, mi, oi])
+# Convert dw from ppm to rad/s. Use the out argument, to pass directly 
to structure.
+multiply( multiply.outer( dw.reshape(1, self.NS), self.nm_no_nd_ones 
), self.frqs, out=self.dw_struct )
+
+# Reshape R20 to per experiment, spin and frequency.
+self.r20_struct[:] = multiply.outer( r1rho_prime.reshape(self.NE, 
self.NS, self.NM), self.no_nd_ones )
+
+# Back calculate the R2eff values.
+ns_r1rho_2site(M0=self.M0, matrix=self.matrix, 
r1rho_prime=self.r20_struct, omega=self.chemical_shifts, offset=self.offset, 
r1=self.r1, pA=pA, pB=pB, dw=self.dw_struct, k_AB=k_AB, k_BA=k_BA, 
spin_lock_fields=self.spin_lock_omega1, relax_time=self.relax_times, 
inv_relax_time=self.inv_relax_times, back_calc=self.back_calc, 
num_points=self.num_disp_points, num_offsets=self.num_offsets)
+
+# Clean the data for all values, which is left over at the end of 
arrays.
+self.back_calc = self.back_calc*self.disp_struct
+
+## For all missing data points, set the back-calculated value to the 
measured values so that it has no effect on the chi-squared value.
+if self.has_missing:
+# Replace with values.
+self.back_calc[self.mask_replace_blank.mask] = 
self.values[self.mask_replace_blank.mask]
 
 # Return the total chi-squared value.
-return chi2_sum
+return chi2_rankN(self.values, self.back_calc, self.errors)
 
 
 def func_ns_r1rho_3site(self, params):


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r24044 - in /branches/disp_spin_speed: ./ docs/Release_Checklist test_suite/system_tests/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 17:06:56 2014
New Revision: 24044

URL: http://svn.gna.org/viewcvs/relax?rev=24044view=rev
Log:
Merged revisions 24040,24043 via svnmerge from 
svn+ssh://tlin...@svn.gna.org/svn/relax/trunk


  r24040 | bugman | 2014-06-17 15:56:47 +0200 (Tue, 17 Jun 2014) | 9 lines
  
  Fixes for all of the relaxation dispersion system tests which were failing 
with the new minfx code.
  
  Due to the tuning of the log barrier constraint algorithm in minfx in the 
commit at
  http://article.gmane.org/gmane.science.mathematics.minfx.scm/25, many system 
tests needed to be
  slightly adjusted.  Two of the Relax_disp.test_tp02_data_to_* system tests 
were also failing as the
  optimisation can no longer move out of the minimum at pA = 0.5 for one spin 
(due to the low quality
  grid search in the auto-analysis).

  r24043 | bugman | 2014-06-17 17:02:17 +0200 (Tue, 17 Jun 2014) | 3 lines
  
  Updated the release checklist document for the new 1.0.7 release of minfx.


Modified:
branches/disp_spin_speed/   (props changed)
branches/disp_spin_speed/docs/Release_Checklist
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

[This mail would be too long, it was shortened to contain the URLs only.]

Modified: branches/disp_spin_speed/docs/Release_Checklist
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/docs/Release_Checklist?rev=24044r1=24043r2=24044view=diff

Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24044r1=24043r2=24044view=diff


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r24050 - in /branches/disp_spin_speed: ./ specific_analyses/relax_disp/sherekhan.py test_suite/system_tests/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 18:24:27 2014
New Revision: 24050

URL: http://svn.gna.org/viewcvs/relax?rev=24050view=rev
Log:
Merged revisions 24047-24049 via svnmerge from 
svn+ssh://tlin...@svn.gna.org/svn/relax/trunk


  r24047 | bugman | 2014-06-17 17:57:06 +0200 (Tue, 17 Jun 2014) | 7 lines
  
  Fixes for the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system 
test.
  
  The pA parameter is no longer tested for one spin as it moves to random 
values on different
  operating systems and 32 vs. 64-bit systems.  This is because this spin 
experiences no exchange,
  both dw and kex are zero.

  r24048 | bugman | 2014-06-17 18:05:23 +0200 (Tue, 17 Jun 2014) | 5 lines
  
  Decreased the value checking precision in the 
Relax_disp.test_hansen_cpmg_data_to_lm63 system test.
  
  This is to allow the test to pass on certain operating systems and 32-bit 
systems.

  r24049 | bugman | 2014-06-17 18:22:38 +0200 (Tue, 17 Jun 2014) | 7 lines
  
  Modified the precision of the output from the relax_disp.sherekhan_input user 
function.
  
  This is simply to allow the Relax_disp.test_sod1wt_t25_to_sherekhan_input 
system test to pass on
  certain 32-bit systems, as the float output to 15 decimal places is not 
always the same.  This
  system test has been updated for the change.


Modified:
branches/disp_spin_speed/   (props changed)
branches/disp_spin_speed/specific_analyses/relax_disp/sherekhan.py
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

Propchange: branches/disp_spin_speed/
--
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Jun 17 18:24:27 2014
@@ -1 +1 @@
-/trunk:1-24043
+/trunk:1-24049

Modified: branches/disp_spin_speed/specific_analyses/relax_disp/sherekhan.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/specific_analyses/relax_disp/sherekhan.py?rev=24050r1=24049r2=24050view=diff
==
--- branches/disp_spin_speed/specific_analyses/relax_disp/sherekhan.py  
(original)
+++ branches/disp_spin_speed/specific_analyses/relax_disp/sherekhan.py  Tue Jun 
17 18:24:27 2014
@@ -130,7 +130,7 @@
 continue
 
 # Store the data.
-lines.append(%20.15g %20.15g %20.15g\n % (point, 
spins[i].r2eff[param_key], spins[i].r2eff_err[param_key]))
+lines.append(%20.15g %20.13g %20.13g\n % (point, 
spins[i].r2eff[param_key], spins[i].r2eff_err[param_key]))
 
 # No data.
 if len(lines) == 1:

Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24050r1=24049r2=24050view=diff
==
--- branches/disp_spin_speed/test_suite/system_tests/relax_disp.py  
(original)
+++ branches/disp_spin_speed/test_suite/system_tests/relax_disp.py  Tue Jun 
17 18:24:27 2014
@@ -2234,9 +2234,9 @@
 print(%-20s %20.15g %20.15g %20.15g\n % (chi2, spin4.chi2, 
spin70.chi2, spin71.chi2))
 self.assertAlmostEqual(spin4.r2[r20_key1], 1.60463650370664, 2)
 self.assertAlmostEqual(spin4.r2[r20_key2], 1.63221675941434, 3)
-self.assertAlmostEqual(spin4.pA, 0.818979078699935, 3)
-self.assertAlmostEqual(spin4.dw, 5.07483389476542e-14, 3)
-self.assertAlmostEqual(spin4.kex/1, 2.29004732365492e-12/1, 3)
+#self.assertAlmostEqual(spin4.pA, 0.818979078699935, 3)# As dw 
(and kex) is zero, this parameter is not stable.
+self.assertAlmostEqual(spin4.dw, 0.0, 6)
+self.assertAlmostEqual(spin4.kex/1, 0.0, 3)
 self.assertAlmostEqual(spin4.chi2, 26.7356711142038, 3)
 self.assertAlmostEqual(spin70.r2[r20_key1], 6.97268077496405, 3)
 self.assertAlmostEqual(spin70.r2[r20_key2], 9.41028133407727, 3)
@@ -2481,17 +2481,17 @@
 print(%-20s %20.15g %20.15g\n % (chi2, spin70.chi2, spin71.chi2))
 
 # Checks for residue :70.
-self.assertAlmostEqual(spin70.r2[r20_key1], 6.7436229263957)
-self.assertAlmostEqual(spin70.r2[r20_key2], 6.57406788826655)
-self.assertAlmostEqual(spin70.phi_ex, 0.31273301746411)
-self.assertAlmostEqual(spin70.kex/1000, 4723.09901154387/1000)
-self.assertAlmostEqual(spin70.chi2, 363.534044873483)
+self.assertAlmostEqual(spin70.r2[r20_key1], 6.7436229263957, 5)
+self.assertAlmostEqual(spin70.r2[r20_key2], 6.57406788826655, 5)
+self.assertAlmostEqual(spin70.phi_ex, 0.31273301746411, 5)
+self.assertAlmostEqual(spin70.kex/1000, 4723.09901154387/1000, 5)
+self.assertAlmostEqual(spin70.chi2, 363.534044873483, 5)
 
 # Checks for residue :71.
-self.assertAlmostEqual(spin71.r2[r20_key1

r24052 - in /branches/disp_spin_speed: ./ test_suite/system_tests/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 18:46:01 2014
New Revision: 24052

URL: http://svn.gna.org/viewcvs/relax?rev=24052view=rev
Log:
Merged revisions 24051 via svnmerge from 
svn+ssh://tlin...@svn.gna.org/svn/relax/trunk


  r24051 | bugman | 2014-06-17 18:27:39 +0200 (Tue, 17 Jun 2014) | 6 lines
  
  Modified the Relax_disp.test_sprangers_data_to_mmq_cr72 system test to pass 
on certain systems.
  
  This test fails on 32-bit Linux (and probably other systems as well).  To fix 
the test, the kex
  values are all divided by 100 before checking them to 4 decimal places of 
accuracy.


Modified:
branches/disp_spin_speed/   (props changed)
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

Propchange: branches/disp_spin_speed/
--
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Jun 17 18:46:01 2014
@@ -1 +1 @@
-/trunk:1-24049
+/trunk:1-24051

Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24052r1=24051r2=24052view=diff
==
--- branches/disp_spin_speed/test_suite/system_tests/relax_disp.py  
(original)
+++ branches/disp_spin_speed/test_suite/system_tests/relax_disp.py  Tue Jun 
17 18:46:01 2014
@@ -5434,7 +5434,7 @@
 self.assertAlmostEqual(spin135S.pA, 0.836591714049569, 4)
 self.assertAlmostEqual(spin135S.dw, 0.583003004605869, 4)
 self.assertAlmostEqual(spin135S.dwH, 0.0361441894065963, 4)
-self.assertAlmostEqual(spin135S.kex, 241.806464344233, 4)
+self.assertAlmostEqual(spin135S.kex/100, 241.806464344233/100, 4)
 self.assertAlmostEqual(spin135S.chi2, 12.4224060116473, 4)
 
 # Checks for residue :135F.
@@ -5443,7 +5443,7 @@
 self.assertAlmostEqual(spin135F.pA, 0.836591714049569, 4)
 self.assertAlmostEqual(spin135F.dw, 0.805849748711916, 4)
 self.assertAlmostEqual(spin135F.dwH, 0.0215791669142752, 4)
-self.assertAlmostEqual(spin135F.kex, 241.806464344233, 4)
+self.assertAlmostEqual(spin135F.kex/100, 241.806464344233/100, 4)
 self.assertAlmostEqual(spin135F.chi2, 12.4224060116473, 4)
 
 # Checks for residue :137S.
@@ -5452,7 +5452,7 @@
 self.assertAlmostEqual(spin137S.pA, 0.836591714049569, 4)
 self.assertAlmostEqual(spin137S.dw, 0.688107406812537, 4)
 self.assertAlmostEqual(spin137S.dwH, 0.034446357344577, 4)
-self.assertAlmostEqual(spin137S.kex, 241.806464344233, 4)
+self.assertAlmostEqual(spin137S.kex/100, 241.806464344233/100, 4)
 self.assertAlmostEqual(spin137S.chi2, 12.4224060116473, 4)
 
 # Checks for residue :137F.
@@ -5461,7 +5461,7 @@
 self.assertAlmostEqual(spin137F.pA, 0.836591714049569, 4)
 self.assertAlmostEqual(spin137F.dw, 0.94978325541294, 4)
 self.assertAlmostEqual(spin137F.dwH, 1.5189362257653e-07, 4)
-self.assertAlmostEqual(spin137F.kex, 241.806464344233, 4)
+self.assertAlmostEqual(spin137F.kex/100, 241.806464344233/100, 4)
 self.assertAlmostEqual(spin137F.chi2, 12.4224060116473, 4)
 
 


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r24053 - /branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 19:04:51 2014
New Revision: 24053

URL: http://svn.gna.org/viewcvs/relax?rev=24053view=rev
Log:
Fatal fix for calling inv_relax_time from relax_time variable.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py?rev=24053r1=24052r2=24053view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   Tue Jun 17 
19:04:51 2014
@@ -116,7 +116,7 @@
 r1rho_prime_i = r1rho_prime[0, si, mi, oi]
 spin_lock_fields_i = spin_lock_fields[0, si, mi, oi]
 relax_time_i = relax_time[0, si, mi, oi]
-inv_relax_time_i = relax_time[0, si, mi, oi]
+inv_relax_time_i = inv_relax_time[0, si, mi, oi]
 back_calc_i = back_calc[0, si, mi, oi]
 num_points_i = num_points[0, si, mi, oi]
 


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r24054 - in /branches/disp_spin_speed: lib/dispersion/ns_r1rho_2site.py target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 19:08:19 2014
New Revision: 24054

URL: http://svn.gna.org/viewcvs/relax?rev=24054view=rev
Log:
Removal of the temporary offset argument.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py?rev=24054r1=24053r2=24054view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   Tue Jun 17 
19:08:19 2014
@@ -58,7 +58,7 @@
 from lib.linear_algebra.matrix_exponential import matrix_exponential
 
 
-def ns_r1rho_2site(M0=None, matrix=None, r1rho_prime=None, omega=None, 
offset=None, r1=0.0, pA=None, pB=None, dw=None, k_AB=None, k_BA=None, 
spin_lock_fields=None, relax_time=None, inv_relax_time=None, back_calc=None, 
num_points=None, num_offsets=None):
+def ns_r1rho_2site(M0=None, matrix=None, r1rho_prime=None, omega=None, 
offset=None, r1=0.0, pA=None, pB=None, dw=None, k_AB=None, k_BA=None, 
spin_lock_fields=None, relax_time=None, inv_relax_time=None, back_calc=None, 
num_points=None):
 The 2-site numerical solution to the Bloch-McConnell equation for R1rho 
data.
 
 This function calculates and stores the R1rho values.
@@ -106,7 +106,7 @@
 # Loop over the spectrometer frequencies.
 for mi in range(NM):
 # Loop over offsets:
-for oi in range(num_offsets[0, si, mi]):
+for oi in range(NO):
 
 omega_i = omega[0, si, mi, oi, 0]
 offset_i = offset[0, si, mi, oi, 0]

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24054r1=24053r2=24054view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 
19:08:19 2014
@@ -1662,7 +1662,7 @@
 self.r20_struct[:] = multiply.outer( r1rho_prime.reshape(self.NE, 
self.NS, self.NM), self.no_nd_ones )
 
 # Back calculate the R2eff values.
-ns_r1rho_2site(M0=self.M0, matrix=self.matrix, 
r1rho_prime=self.r20_struct, omega=self.chemical_shifts, offset=self.offset, 
r1=self.r1, pA=pA, pB=pB, dw=self.dw_struct, k_AB=k_AB, k_BA=k_BA, 
spin_lock_fields=self.spin_lock_omega1, relax_time=self.relax_times, 
inv_relax_time=self.inv_relax_times, back_calc=self.back_calc, 
num_points=self.num_disp_points, num_offsets=self.num_offsets)
+ns_r1rho_2site(M0=self.M0, matrix=self.matrix, 
r1rho_prime=self.r20_struct, omega=self.chemical_shifts, offset=self.offset, 
r1=self.r1, pA=pA, pB=pB, dw=self.dw_struct, k_AB=k_AB, k_BA=k_BA, 
spin_lock_fields=self.spin_lock_omega1, relax_time=self.relax_times, 
inv_relax_time=self.inv_relax_times, back_calc=self.back_calc, 
num_points=self.num_disp_points)
 
 # Clean the data for all values, which is left over at the end of 
arrays.
 self.back_calc = self.back_calc*self.disp_struct


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r24055 - /branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 19:11:07 2014
New Revision: 24055

URL: http://svn.gna.org/viewcvs/relax?rev=24055view=rev
Log:
Documentation fix for the dimensionality of the input arrays.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py?rev=24055r1=24054r2=24055view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   Tue Jun 17 
19:11:07 2014
@@ -69,33 +69,33 @@
 @keyword matrix:A numpy array to be populated to create the 
evolution matrix.
 @type matrix:   numpy rank-2, 6D float64 array
 @keyword r1rho_prime:   The R1rho_prime parameter value (R1rho with no 
exchange).
-@type r1rho_prime:  float
+@type r1rho_prime:  numpy float array of rank [NS][NM][NO][ND]
 @keyword omega: The chemical shift for the spin in rad/s.
-@type omega:float
+@type omega:numpy float array of rank [NS][NM][NO][ND]
 @keyword offset:The spin-lock offsets for the data.
-@type offset:   numpy rank-1 float array
+@type offset:   numpy float array of rank [NS][NM][NO][ND]
 @keyword r1:The R1 relaxation rate.
-@type r1:   float
+@type r1:   numpy float array of rank [NS][NM][NO][ND]
 @keyword pA:The population of state A.
 @type pA:   float
 @keyword pB:The population of state B.
 @type pB:   float
 @keyword dw:The chemical exchange difference between 
states A and B in rad/s.
-@type dw:   float
+@type dw:   numpy float array of rank [NS][NM][NO][ND]
 @keyword k_AB:  The rate of exchange from site A to B (rad/s).
 @type k_AB: float
 @keyword k_BA:  The rate of exchange from site B to A (rad/s).
 @type k_BA: float
 @keyword spin_lock_fields:  The R1rho spin-lock field strengths (in 
rad.s^-1).
-@type spin_lock_fields: numpy rank-1 float array
+@type spin_lock_fields: numpy float array of rank [NS][NM][NO][ND]
 @keyword relax_time:The total relaxation time period for each 
spin-lock field strength (in seconds).
-@type relax_time:   float
+@type relax_time:   numpy float array of rank [NS][NM][NO][ND]
 @keyword inv_relax_time:The inverse of the relaxation time period for 
each spin-lock field strength (in inverse seconds).  This is used for faster 
calculations.
-@type inv_relax_time:   float
+@type inv_relax_time:   numpy float array of rank [NS][NM][NO][ND]
 @keyword back_calc: The array for holding the back calculated 
R2eff values.  Each element corresponds to one of the CPMG nu1 frequencies.
-@type back_calc:numpy rank-1 float array
+@type back_calc:numpy float array of rank [NS][NM][NO][ND]
 @keyword num_points:The number of points on the dispersion curve, 
equal to the length of the tcp and back_calc arguments.
-@type num_points:   int
+@type num_points:   numpy int array of rank [NS][NM][NO]
 
 
 # Extract shape of experiment.


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r24056 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 19:27:10 2014
New Revision: 24056

URL: http://svn.gna.org/viewcvs/relax?rev=24056view=rev
Log:
Implemented the target function for ns r1rho 3site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24056r1=24055r2=24056view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 
19:27:10 2014
@@ -784,35 +784,26 @@
 k_AC = pC * kex_AC / pA_pC
 dw_AC = dw_AB + dw_BC
 
-# Initialise.
-chi2_sum = 0.0
-
-# Loop over the spins.
-for si in range(self.num_spins):
-# Loop over the spectrometer frequencies.
-for mi in range(self.num_frq):
-# The R20 index.
-r20_index = mi + si*self.num_frq
-
-# Convert dw from ppm to rad/s.
-dw_AB_frq = dw_AB[si] * self.frqs[0, si, mi, 0, 0]
-dw_AC_frq = dw_AC[si] * self.frqs[0, si, mi, 0, 0]
-
-# Loop over the offsets.
-for oi in range(self.num_offsets[0, si, mi]):
-# Back calculate the R2eff values for each experiment type.
-ns_r1rho_3site(M0=self.M0, matrix=self.matrix, 
r1rho_prime=r1rho_prime[r20_index], omega=self.chemical_shifts[0, si, mi, oi, 
0], offset=self.offset[0, si, mi, oi, 0], r1=self.r1[0, si, mi, oi, 0], pA=pA, 
pB=pB, pC=pC, dw_AB=dw_AB_frq, dw_AC=dw_AC_frq, k_AB=k_AB, k_BA=k_BA, 
k_BC=k_BC, k_CB=k_CB, k_AC=k_AC, k_CA=k_CA, 
spin_lock_fields=self.spin_lock_omega1[0, si, mi, oi], 
relax_time=self.relax_times[0, si, mi, oi], 
inv_relax_time=self.inv_relax_times[0, si, mi, oi], back_calc=self.back_calc[0, 
si, mi, oi], num_points=self.num_disp_points[0, si, mi, oi])
-
-# For all missing data points, set the back-calculated 
value to the measured values so that it has no effect on the chi-squared value.
-for di in range(self.num_disp_points[0, si, mi, oi]):
-if self.missing[0, si, mi, oi, di]:
-self.back_calc[0, si, mi, oi, di] = self.values[0, 
si, mi, oi, di]
-
-# Calculate and return the chi-squared value.
-chi2_sum += chi2(self.values[0, si, mi, oi], 
self.back_calc[0, si, mi, oi], self.errors[0, si, mi, oi])
+# Convert dw from ppm to rad/s. Use the out argument, to pass directly 
to structure.
+multiply( multiply.outer( dw_AB.reshape(1, self.NS), 
self.nm_no_nd_ones ), self.frqs, out=self.dw_AB_struct )
+multiply( multiply.outer( dw_AC.reshape(1, self.NS), 
self.nm_no_nd_ones ), self.frqs, out=self.dw_AC_struct )
+
+# Reshape R20 to per experiment, spin and frequency.
+self.r20_struct[:] = multiply.outer( r1rho_prime.reshape(self.NE, 
self.NS, self.NM), self.no_nd_ones )
+
+# Back calculate the R2eff values for each experiment type.
+ns_r1rho_3site(M0=self.M0, matrix=self.matrix, 
r1rho_prime=self.r20_struct, omega=self.chemical_shifts, offset=self.offset, 
r1=self.r1, pA=pA, pB=pB, pC=pC, dw_AB=self.dw_AB_struct, 
dw_AC=self.dw_AC_struct, k_AB=k_AB, k_BA=k_BA, k_BC=k_BC, k_CB=k_CB, k_AC=k_AC, 
k_CA=k_CA, spin_lock_fields=self.spin_lock_omega1, relax_time=self.relax_times, 
inv_relax_time=self.inv_relax_times, back_calc=self.back_calc, 
num_points=self.num_disp_points)
+
+# Clean the data for all values, which is left over at the end of 
arrays.
+self.back_calc = self.back_calc*self.disp_struct
+
+## For all missing data points, set the back-calculated value to the 
measured values so that it has no effect on the chi-squared value.
+if self.has_missing:
+# Replace with values.
+self.back_calc[self.mask_replace_blank.mask] = 
self.values[self.mask_replace_blank.mask]
 
 # Return the total chi-squared value.
-return chi2_sum
+return chi2_rankN(self.values, self.back_calc, self.errors)
 
 
 def experiment_type_setup(self):


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r24057 - /branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 19:27:12 2014
New Revision: 24057

URL: http://svn.gna.org/viewcvs/relax?rev=24057view=rev
Log:
Implemented the lib function for ns r1rho 3site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py?rev=24057r1=24056r2=24057view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py   (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py   Tue Jun 17 
19:27:12 2014
@@ -75,13 +75,13 @@
 @keyword matrix:A numpy array to be populated to create the 
evolution matrix.
 @type matrix:   numpy rank-2, 9D float64 array
 @keyword r1rho_prime:   The R1rho_prime parameter value (R1rho with no 
exchange).
-@type r1rho_prime:  float
+@type r1rho_prime:  numpy float array of rank [NS][NM][NO][ND]
 @keyword omega: The chemical shift for the spin in rad/s.
-@type omega:float
+@type omega:numpy float array of rank [NS][NM][NO][ND]
 @keyword offset:The spin-lock offsets for the data.
-@type offset:   numpy rank-1 float array
+@type offset:   numpy float array of rank [NS][NM][NO][ND]
 @keyword r1:The R1 relaxation rate.
-@type r1:   float
+@type r1:   numpy float array of rank [NS][NM][NO][ND]
 @keyword pA:The population of state A.
 @type pA:   float
 @keyword pB:The population of state B.
@@ -89,9 +89,9 @@
 @keyword pC:The population of state C.
 @type pC:   float
 @keyword dw_AB: The chemical exchange difference between 
states A and B in rad/s.
-@type dw_AB:float
+@type dw_AB:numpy float array of rank [NS][NM][NO][ND]
 @keyword dw_AC: The chemical exchange difference between 
states A and C in rad/s.
-@type dw_AC:float
+@type dw_AC:numpy float array of rank [NS][NM][NO][ND]
 @keyword k_AB:  The rate of exchange from site A to B (rad/s).
 @type k_AB: float
 @keyword k_BA:  The rate of exchange from site B to A (rad/s).
@@ -105,45 +105,68 @@
 @keyword k_CA:  The rate of exchange from site C to A (rad/s).
 @type k_CA: float
 @keyword spin_lock_fields:  The R1rho spin-lock field strengths (in 
rad.s^-1).
-@type spin_lock_fields: numpy rank-1 float array
+@type spin_lock_fields: numpy float array of rank [NS][NM][NO][ND]
 @keyword relax_time:The total relaxation time period for each 
spin-lock field strength (in seconds).
-@type relax_time:   float
+@type relax_time:   numpy float array of rank [NS][NM][NO][ND]
 @keyword inv_relax_time:The inverse of the relaxation time period for 
each spin-lock field strength (in inverse seconds).  This is used for faster 
calculations.
-@type inv_relax_time:   float
+@type inv_relax_time:   numpy float array of rank [NS][NM][NO][ND]
 @keyword back_calc: The array for holding the back calculated 
R2eff values.  Each element corresponds to one of the CPMG nu1 frequencies.
-@type back_calc:numpy rank-1 float array
+@type back_calc:numpy float array of rank [NS][NM][NO][ND]
 @keyword num_points:The number of points on the dispersion curve, 
equal to the length of the tcp and back_calc arguments.
-@type num_points:   int
+@type num_points:   numpy int array of rank [NS][NM][NO]
 
 
-# Repetitive calculations (to speed up calculations).
-Wa = omega  # Larmor frequency for state A [s^-1].
-Wb = omega + dw_AB  # Larmor frequency for state B [s^-1].
-Wc = omega + dw_AC  # Larmor frequency for state C [s^-1].
-W = pA*Wa + pB*Wb + pC*Wc   # Population-averaged Larmor frequency [s^-1].
-dA = Wa - offset# Offset of spin-lock from A.
-dB = Wb - offset# Offset of spin-lock from B.
-dC = Wc - offset# Offset of spin-lock from C.
-d = W - offset  # Offset of spin-lock from population-average.
+# Extract shape of experiment.
+NE, NS, NM, NO = num_points.shape
 
-# Loop over the time points, back calculating the R2eff values.
-for i in range(num_points):
-# The matrix that contains all the contributions to the evolution, 
i.e. relaxation, exchange and chemical shift

r24059 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 20:26:37 2014
New Revision: 24059

URL: http://svn.gna.org/viewcvs/relax?rev=24059view=rev
Log:
Implemented target function for LM63 3site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24059r1=24058r2=24059view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 
20:26:37 2014
@@ -234,6 +234,8 @@
 self.dwH_AB_struct = deepcopy(numpy_array_zeros)
 self.dwH_AC_struct = deepcopy(numpy_array_zeros)
 self.phi_ex_struct = deepcopy(numpy_array_zeros)
+self.phi_ex_B_struct = deepcopy(numpy_array_zeros)
+self.phi_ex_C_struct = deepcopy(numpy_array_zeros)
 
 # Structure of values, errors and missing.
 self.values = deepcopy(numpy_array_zeros)
@@ -1060,34 +1062,26 @@
 quart_kB = kB / 4.0
 quart_kC = kC / 4.0
 
-# Initialise.
-chi2_sum = 0.0
-
-# Loop over the spins.
-for si in range(self.num_spins):
-# Loop over the spectrometer frequencies.
-for mi in range(self.num_frq):
-# The R20 index.
-r20_index = mi + si*self.num_frq
-
-# Convert phi_ex (or rex) from ppm^2 to (rad/s)^2.
-rex_B_scaled = rex_B[si] * self.frqs_squared[0, si, mi, 0, 0]
-rex_C_scaled = rex_C[si] * self.frqs_squared[0, si, mi, 0, 0]
-
-# Back calculate the R2eff values.
-r2eff_LM63_3site(r20=R20[r20_index], rex_B=rex_B_scaled, 
rex_C=rex_C_scaled, quart_kB=quart_kB, quart_kC=quart_kC, 
cpmg_frqs=self.cpmg_frqs[0, si, mi, 0], back_calc=self.back_calc[0, si, mi, 0], 
num_points=self.num_disp_points[0, si, mi, 0])
-
-# For all missing data points, set the back-calculated value 
to the measured values so that it has no effect on the chi-squared value.
-for di in range(self.num_disp_points[0, si, mi, 0]):
-if self.missing[0, si, mi, 0, di]:
-self.back_calc[0, si, mi, 0, di] = self.values[0, si, 
mi, 0, di]
-
-# Calculate and return the chi-squared value.
-chi2_sum += chi2(self.values[0, si, mi, 0], self.back_calc[0, 
si, mi, 0], self.errors[0, si, mi, 0])
+# Convert phi_ex (or rex) from ppm^2 to (rad/s)^2.
+multiply( multiply.outer( rex_B.reshape(1, self.NS), 
self.nm_no_nd_ones ), self.frqs_squared, out=self.phi_ex_B_struct )
+multiply( multiply.outer( rex_C.reshape(1, self.NS), 
self.nm_no_nd_ones ), self.frqs_squared, out=self.phi_ex_C_struct )
+
+# Reshape R20 to per experiment, spin and frequency.
+self.r20_struct[:] = multiply.outer( R20.reshape(self.NE, self.NS, 
self.NM), self.no_nd_ones )
+
+# Back calculate the R2eff values.
+r2eff_LM63_3site(r20=self.r20_struct, rex_B=self.phi_ex_B_struct, 
rex_C=self.phi_ex_C_struct, quart_kB=quart_kB, quart_kC=quart_kC, 
cpmg_frqs=self.cpmg_frqs, back_calc=self.back_calc, 
num_points=self.num_disp_points)
+
+# Clean the data for all values, which is left over at the end of 
arrays.
+self.back_calc = self.back_calc*self.disp_struct
+
+## For all missing data points, set the back-calculated value to the 
measured values so that it has no effect on the chi-squared value.
+if self.has_missing:
+# Replace with values.
+self.back_calc[self.mask_replace_blank.mask] = 
self.values[self.mask_replace_blank.mask]
 
 # Return the total chi-squared value.
-return chi2_sum
-
+return chi2_rankN(self.values, self.back_calc, self.errors)
 
 def func_LM63(self, params):
 Target function for the Luz and Meiboom (1963) fast 2-site exchange 
model.


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r24061 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 20:26:41 2014
New Revision: 24061

URL: http://svn.gna.org/viewcvs/relax?rev=24061view=rev
Log:
Removed the number of disp points in target function for LM63 3site, since it 
is no Ãlonger used,
but have been replaced with mask replacements.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24061r1=24060r2=24061view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Tue Jun 17 
20:26:41 2014
@@ -1070,7 +1070,7 @@
 self.r20_struct[:] = multiply.outer( R20.reshape(self.NE, self.NS, 
self.NM), self.no_nd_ones )
 
 # Back calculate the R2eff values.
-r2eff_LM63_3site(r20=self.r20_struct, rex_B=self.phi_ex_B_struct, 
rex_C=self.phi_ex_C_struct, quart_kB=quart_kB, quart_kC=quart_kC, 
cpmg_frqs=self.cpmg_frqs, back_calc=self.back_calc, 
num_points=self.num_disp_points)
+r2eff_LM63_3site(r20=self.r20_struct, rex_B=self.phi_ex_B_struct, 
rex_C=self.phi_ex_C_struct, quart_kB=quart_kB, quart_kC=quart_kC, 
cpmg_frqs=self.cpmg_frqs, back_calc=self.back_calc)
 
 # Clean the data for all values, which is left over at the end of 
arrays.
 self.back_calc = self.back_calc*self.disp_struct


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r24060 - /branches/disp_spin_speed/lib/dispersion/lm63_3site.py

[tlinnet]

Author: tlinnet
Date: Tue Jun 17 20:26:39 2014
New Revision: 24060

URL: http://svn.gna.org/viewcvs/relax?rev=24060view=rev
Log:
Implemented the lib function for LM63 3site, for higher dimensional data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/lm63_3site.py

Modified: branches/disp_spin_speed/lib/dispersion/lm63_3site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/lm63_3site.py?rev=24060r1=24059r2=24060view=diff
==
--- branches/disp_spin_speed/lib/dispersion/lm63_3site.py   (original)
+++ branches/disp_spin_speed/lib/dispersion/lm63_3site.py   Tue Jun 17 
20:26:39 2014
@@ -64,45 +64,74 @@
 
 
 # Python module imports.
-from math import tanh
+from numpy import any, fabs, min, tanh, isfinite, sum
+from numpy.ma import fix_invalid, masked_where
 
 
-def r2eff_LM63_3site(r20=None, rex_B=None, rex_C=None, quart_kB=None, 
quart_kC=None, cpmg_frqs=None, back_calc=None, num_points=None):
+def r2eff_LM63_3site(r20=None, rex_B=None, rex_C=None, quart_kB=None, 
quart_kC=None, cpmg_frqs=None, back_calc=None):
 Calculate the R2eff values for the LM63 3-site model.
 
 See the module docstring for details.
 
 
 @keyword r20:   The R20 parameter value (R2 with no exchange).
-@type r20:  float
+@type r20:  numpy float array of rank [NS][NM][NO][ND]
 @keyword rex_B: The phi_ex_B / kB parameter value.
-@type rex_B:float
+@type rex_B:numpy float array of rank [NS][NM][NO][ND]
 @keyword rex_C: The phi_ex_C / kC parameter value.
-@type rex_C:float
+@type rex_C:numpy float array of rank [NE][NS][NM][NO][ND]
 @keyword quart_kB:  Approximate chemical exchange rate constant 
between sites A and B (the exchange rate in rad/s) divided by 4.
 @type quart_kB: float
 @keyword quart_kC:  Approximate chemical exchange rate constant 
between sites A and C (the exchange rate in rad/s) divided by 4.
 @type quart_kC: float
 @keyword cpmg_frqs: The CPMG nu1 frequencies.
-@type cpmg_frqs:numpy rank-1 float array
+@type cpmg_frqs:numpy float array of rank [NE][NS][NM][NO][ND]
 @keyword back_calc: The array for holding the back calculated R2eff 
values.  Each element corresponds to one of the CPMG nu1 frequencies.
-@type back_calc:numpy rank-1 float array
-@keyword num_points:The number of points on the dispersion curve, 
equal to the length of the cpmg_frqs and back_calc arguments.
-@type num_points:   int
+@type back_calc:numpy float array of rank [NE][NS][NM][NO][ND]
 
 
-# Loop over the time points, back calculating the R2eff values.
-for i in range(num_points):
-# Catch zeros.
-if rex_B == 0.0 and rex_C == 0.0:
-back_calc[i] = r20
+# Flag to tell if values should be replaced.
+t_rex_zero = False
+t_quart_kB_zero = False
+t_quart_kC_zero = False
+t_quart_kB_kC_zero = False
 
-# Avoid divide by zero.
-elif quart_kB == 0.0 or quart_kC == 0.0:
-back_calc[i] = 1e100
+# Avoid divide by zero.
+if quart_kB == 0.0:
+t_quart_kB_zero = True
 
-# The full formula.
-else:
-back_calc[i] = r20
-back_calc[i] += rex_B * (1.0 - cpmg_frqs[i] * tanh(quart_kB / 
cpmg_frqs[i]) / quart_kB)
-back_calc[i] += rex_C * (1.0 - cpmg_frqs[i] * tanh(quart_kC / 
cpmg_frqs[i]) / quart_kC)
+if quart_kC == 0.0:
+t_quart_kC_zero = True
+
+# Test it both is zero.
+if t_quart_kB_zero and t_quart_kC_zero:
+t_quart_kB_kC_zero = True
+
+# Test if rex is zero. Wait for replacement, since this is spin specific.
+if min(fabs(rex_B)) == 0.0 and min(fabs(rex_C)) == 0.0:
+t_rex_zero = True
+mask_rex_B_zero = masked_where(rex_B == 0.0, rex_B)
+mask_rex_C_zero = masked_where(rex_C == 0.0, rex_C)
+
+# Replace data in array.
+# If both quart_kB and quart_kC is zero.
+if t_quart_kB_kC_zero:
+back_calc[:] = r20
+elif t_quart_kB_zero:
+back_calc[:] = r20 + rex_C * (1.0 - cpmg_frqs * tanh(quart_kC / 
cpmg_frqs) / quart_kC)
+elif t_quart_kC_zero:
+back_calc[:] = r20 + rex_B * (1.0 - cpmg_frqs * tanh(quart_kB / 
cpmg_frqs) / quart_kB)
+else:
+# Calc R2eff.
+back_calc[:] = r20 + rex_B * (1.0 - cpmg_frqs * tanh(quart_kB / 
cpmg_frqs) / quart_kB) + rex_C * (1.0 - cpmg_frqs * tanh(quart_kC / cpmg_frqs) 
/ quart_kC)
+
+# If rex is zero.
+if t_rex_zero:
+back_calc[mask_rex_B_zero.mask] = r20[mask_rex_B_zero.mask]
+back_calc[mask_rex_C_zero.mask] = r20[mask_rex_C_zero.mask]
+
+# Catch errors, taking a sum over

r24064 - /branches/disp_spin_speed/specific_analyses/relax_disp/data.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 09:25:49 2014
New Revision: 24064

URL: http://svn.gna.org/viewcvs/relax?rev=24064view=rev
Log:
Removed superfluous check, after the returned data is now in right structure.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/specific_analyses/relax_disp/data.py

Modified: branches/disp_spin_speed/specific_analyses/relax_disp/data.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/specific_analyses/relax_disp/data.py?rev=24064r1=24063r2=24064view=diff
==
--- branches/disp_spin_speed/specific_analyses/relax_disp/data.py   
(original)
+++ branches/disp_spin_speed/specific_analyses/relax_disp/data.py   Wed Jun 
18 09:25:49 2014
@@ -1854,9 +1854,6 @@
 
 # Loop over the dispersion points.
 for di in range(len(back_calc[ei][0][mi][oi])):
-# Back calc can have more points in end of array.
-if di  len(cpmg_frqs_new[ei][mi][oi]) - 1:
-continue
 # Skip invalid points (values of 1e100).
 if back_calc[ei][0][mi][oi][di]  1e50:
 continue


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r24063 - /branches/disp_spin_speed/specific_analyses/relax_disp/optimisation.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 09:25:48 2014
New Revision: 24063

URL: http://svn.gna.org/viewcvs/relax?rev=24063view=rev
Log:
Used the new class function: get_back_calc(), to get the data in the right 
structures when interpolating for graphs.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/specific_analyses/relax_disp/optimisation.py

Modified: branches/disp_spin_speed/specific_analyses/relax_disp/optimisation.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/specific_analyses/relax_disp/optimisation.py?rev=24063r1=24062r2=24063view=diff
==
--- branches/disp_spin_speed/specific_analyses/relax_disp/optimisation.py   
(original)
+++ branches/disp_spin_speed/specific_analyses/relax_disp/optimisation.py   
Wed Jun 18 09:25:48 2014
@@ -192,7 +192,7 @@
 spin.chi2 = chi2
 
 # Return the structure.
-return model.back_calc
+return model.get_back_calc()
 
 
 def calculate_r2eff():


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r24062 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 09:25:45 2014
New Revision: 24062

URL: http://svn.gna.org/viewcvs/relax?rev=24062view=rev
Log:
Implemented class function in target class, to return back_calc values as list 
of lists.

This is the back and forth conversion between the data structures implemented 
when gathering the data,
and the data send to the library function of higher dimensionality.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24062r1=24061r2=24062view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Wed Jun 18 
09:25:45 2014
@@ -55,7 +55,7 @@
 from lib.errors import RelaxError
 from lib.float import isNaN
 from target_functions.chi2 import chi2, chi2_rankN
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ, 
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ, 
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_R1RHO, MODEL_B14, MODEL_B14_FULL, 
MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, MODEL_IT99, MODEL_LIST_CPMG, 
MODEL_LIST_CPMG_FULL, MODEL_LIST_FULL, MODEL_LIST_MMQ, MODEL_LIST_MQ_CPMG, 
MODEL_LIST_R1RHO, MODEL_LIST_R1RHO_FULL, MODEL_LM63, MODEL_LM63_3SITE, 
MODEL_M61, MODEL_M61B, MODEL_MP05, MODEL_MMQ_CR72, MODEL_NOREX, 
MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, 
MODEL_NS_CPMG_2SITE_EXPANDED, MODEL_NS_CPMG_2SITE_STAR, 
MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, MODEL_NS_MMQ_3SITE, 
MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, MODEL_NS_R1RHO_3SITE, 
MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_TAP03, MODEL_TP02, MODEL_TSMFK01
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_DQ, 
EXP_TYPE_CPMG_MQ, EXP_TYPE_CPMG_PROTON_MQ, EXP_TYPE_CPMG_PROTON_SQ, 
EXP_TYPE_CPMG_SQ, EXP_TYPE_CPMG_ZQ, EXP_TYPE_LIST_CPMG, EXP_TYPE_R1RHO, 
MODEL_B14, MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_DPL94, 
MODEL_IT99, MODEL_LIST_CPMG, MODEL_LIST_CPMG_FULL, MODEL_LIST_FULL, 
MODEL_LIST_MMQ, MODEL_LIST_MQ_CPMG, MODEL_LIST_R1RHO, MODEL_LIST_R1RHO_FULL, 
MODEL_LM63, MODEL_LM63_3SITE, MODEL_M61, MODEL_M61B, MODEL_MP05, 
MODEL_MMQ_CR72, MODEL_NOREX, MODEL_NS_CPMG_2SITE_3D, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, 
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL, MODEL_NS_MMQ_2SITE, 
MODEL_NS_MMQ_3SITE, MODEL_NS_MMQ_3SITE_LINEAR, MODEL_NS_R1RHO_2SITE, 
MODEL_NS_R1RHO_3SITE, MODEL_NS_R1RHO_3SITE_LINEAR, MODEL_TAP03, MODEL_TP02, 
MODEL_TSMFK01
 
 
 class Dispersion:
@@ -172,6 +172,9 @@
 self.num_frq = num_frq
 self.exp_types = exp_types
 self.scaling_matrix = scaling_matrix
+self.values_orig = values
+self.cpmg_frqs_orig = cpmg_frqs
+self.spin_lock_nu1_orig = spin_lock_nu1
 
 ### Initialise higher order numpy structures.
 # Define the shape of all the numpy arrays.
@@ -1831,3 +1834,28 @@
 
 # Return the total chi-squared value.
 return chi2_rankN(self.values, self.back_calc, self.errors)
+
+def get_back_calc(self):
+Class function to return back_calc as lists of lists.  Number of 
values in should match number of dispersion points or spin_lock.
+
+@return:back_calc in structure of list of lists.
+@rtype: float
+
+
+back_calc_return = deepcopy(self.values_orig)
+
+# Loop over experiments
+for ei in range(self.NE):
+exp_type = self.exp_types[ei]
+for si in range(self.NS):
+for mi in range(self.NM):
+for oi in range(self.NO):
+back_calc_return[ei][si][mi].append([])
+if exp_type in EXP_TYPE_LIST_CPMG:
+num = len(self.cpmg_frqs_orig[ei][mi][oi])
+else:
+num = len(self.spin_lock_nu1_orig[ei][mi][oi])
+back_calc_return[ei][si][mi][oi][:] = 
self.back_calc[ei, si, mi, oi, :num]
+
+return back_calc_return
+


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r24065 - /branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 09:41:11 2014
New Revision: 24065

URL: http://svn.gna.org/viewcvs/relax?rev=24065view=rev
Log:
Made changes to the dir argument of systemtest Relax_disp.test_r1rho_kjaergaard.

This is to prepare for:
sr #3124 (https://gna.org/support/?3124): Grace graphs production for R1rho 
analysis with R2_eff as function of Omega_eff
sr #3138 (https://gna.org/support/?3138): Interpolating theta through spin-lock 
offset [Omega], rather than spin-lock field strength [w1]

This is also to test an expected bug, if R1 is not loaded.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

[This mail would be too long, it was shortened to contain the URLs only.]

Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24065r1=24064r2=24065view=diff


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r24071 - /branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 10:30:02 2014
New Revision: 24071

URL: http://svn.gna.org/viewcvs/relax?rev=24071view=rev
Log:
Split systemtest test_r1rho_kjaergaard into test_r1rho_kjaergaard_auto and 
test_r1rho_kjaergaard_man.

This is to test use of the manual way to analyse.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

[This mail would be too long, it was shortened to contain the URLs only.]

Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24071r1=24070r2=24071view=diff


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r24070 - /branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 10:30:00 2014
New Revision: 24070

URL: http://svn.gna.org/viewcvs/relax?rev=24070view=rev
Log:
Renamed systemtes test_r1rho_kjaergaard to test_r1rho_kjaergaard_auto.

This corresponds to the use of the automatic analysis method.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24070r1=24069r2=24070view=diff
==
--- branches/disp_spin_speed/test_suite/system_tests/relax_disp.py  
(original)
+++ branches/disp_spin_speed/test_suite/system_tests/relax_disp.py  Wed Jun 
18 10:30:00 2014
@@ -58,7 +58,7 @@
 
test_bug_21344_sparse_time_spinlock_acquired_r1rho_fail_relax_disp,
 test_exp_fit,
 test_m61_exp_data_to_m61,
-test_r1rho_kjaergaard,
+test_r1rho_kjaergaard_auto,
 test_value_write_calc_rotating_frame_params_auto_analysis
 ]
 
@@ -4224,10 +4224,12 @@
 self.assertAlmostEqual(cdp.mol[0].res[0].spin[0].chi2, 
0.030959849811015544, 3)
 
 
-def test_r1rho_kjaergaard(self):
+def test_r1rho_kjaergaard_auto(self):
 Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho 
relaxation dispersion experiments using the 'DPL' model.
 
 This uses the data from Kjaergaard's paper at U{DOI: 
10.1021/bi4001062http://dx.doi.org/10.1021/bi4001062}.
+
+This uses the automatic analysis.
 
 
 


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r24073 - /branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 10:35:42 2014
New Revision: 24073

URL: http://svn.gna.org/viewcvs/relax?rev=24073view=rev
Log:
Implemented systemtest test_r1rho_kjaergaard_missing_r1, for safety check if R1 
data is not loaded.

The systemtest passes, so target function is safe.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/test_suite/system_tests/relax_disp.py

Modified: branches/disp_spin_speed/test_suite/system_tests/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/system_tests/relax_disp.py?rev=24073r1=24072r2=24073view=diff
==
--- branches/disp_spin_speed/test_suite/system_tests/relax_disp.py  
(original)
+++ branches/disp_spin_speed/test_suite/system_tests/relax_disp.py  Wed Jun 
18 10:35:42 2014
@@ -60,6 +60,7 @@
 test_m61_exp_data_to_m61,
 test_r1rho_kjaergaard_auto,
 test_r1rho_kjaergaard_man,
+test_r1rho_kjaergaard_missing_r1,
 test_value_write_calc_rotating_frame_params_auto_analysis
 ]
 
@@ -4587,6 +4588,80 @@
 
self.assert_(access(result_dir_name+sep+'resultsR1'+sep+'final'+sep+'theta.out',
 F_OK))
 
 
+def test_r1rho_kjaergaard_missing_r1(self):
+Optimisation of the Kjaergaard et al., 2013 Off-resonance R1rho 
relaxation dispersion experiments using the 'DPL' model.
+
+This uses the data from Kjaergaard's paper at U{DOI: 
10.1021/bi4001062http://dx.doi.org/10.1021/bi4001062}.
+
+This uses the automatic analysis, with missing loading R1.
+
+
+
+# Cluster residues
+cluster_ids = [
+:13@N,
+:15@N,
+:16@N,
+:25@N,
+:26@N,
+:28@N,
+:39@N,
+:40@N,
+:41@N,
+:43@N,
+:44@N,
+:45@N,
+:49@N,
+:52@N,
+:53@N]
+
+# Load the data.
+self.setup_r1rho_kjaergaard(cluster_ids=cluster_ids, read_R1=False)
+
+# The dispersion models.
+MODELS = ['R2eff', 'DPL94']
+
+# The grid search size (the number of increments per dimension).
+GRID_INC = 4
+
+# The number of Monte Carlo simulations to be used for error analysis 
at the end of the analysis.
+MC_NUM = 3
+
+# Model selection technique.
+MODSEL = 'AIC'
+
+# Execute the auto-analysis (fast).
+# Standard parameters are: func_tol=1e-25, grad_tol=None, 
max_iter=1000,
+OPT_FUNC_TOL = 1e-1
+relax_disp.Relax_disp.opt_func_tol = OPT_FUNC_TOL
+OPT_MAX_ITERATIONS = 1000
+relax_disp.Relax_disp.opt_max_iterations = OPT_MAX_ITERATIONS
+
+result_dir_name = ds.tmpdir
+
+# Make all spins free
+for curspin in cluster_ids:
+self.interpreter.relax_disp.cluster('free spins', curspin)
+# Shut them down
+self.interpreter.deselect.spin(spin_id=curspin, change_all=False)
+
+# Select only a subset of spins for global fitting
+#self.interpreter.select.spin(spin_id=':41@N', change_all=False)
+#self.interpreter.relax_disp.cluster('model_cluster', ':41@N')
+
+#self.interpreter.select.spin(spin_id=':40@N', change_all=False)
+#self.interpreter.relax_disp.cluster('model_cluster', ':40@N')
+
+self.interpreter.select.spin(spin_id=':52@N', change_all=False)
+#self.interpreter.relax_disp.cluster('model_cluster', ':52@N')
+
+# Run the analysis.
+relax_disp.Relax_disp(pipe_name=ds.pipe_name, 
pipe_bundle=ds.pipe_bundle, results_dir=result_dir_name, models=MODELS, 
grid_inc=GRID_INC, mc_sim_num=MC_NUM, modsel=MODSEL)
+
+# Check the kex value of residue 52
+#self.assertAlmostEqual(cdp.mol[0].res[41].spin[0].kex, 
ds.ref[':52@N'][6])
+
+
 def test_r2eff_read(self):
 Test the operation of the relax_disp.r2eff_read user function.
 


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r24075 - /branches/disp_spin_speed/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 10:44:04 2014
New Revision: 24075

URL: http://svn.gna.org/viewcvs/relax?rev=24075view=rev
Log:
Replaced double or triple hash-tags ## with single hash-tags #.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24075r1=24074r2=24075view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Wed Jun 18 
10:44:04 2014
@@ -176,7 +176,7 @@
 self.cpmg_frqs_orig = cpmg_frqs
 self.spin_lock_nu1_orig = spin_lock_nu1
 
-### Initialise higher order numpy structures.
+# Initialise higher order numpy structures.
 # Define the shape of all the numpy arrays.
 # The total numbers of experiments, number of spins, number of 
magnetic field strength, maximum number of offsets, maximum number of 
dispersion point.
 self.NE = len(self.exp_types)
@@ -351,7 +351,7 @@
 # Get the tilt angles.
 self.tilt_angles[ei, si, mi, oi, di] = 
tilt_angles[ei][si][mi][oi][di]
 self.offset[ei, si, mi, oi] = 
offset[ei][si][mi][oi]
-## Convert the spin-lock data to rad.s^-1.
+# Convert the spin-lock data to rad.s^-1.
 self.spin_lock_omega1[ei, si, mi, oi, di] = 
2.0 * pi * spin_lock_nu1[ei][mi][oi][di]
 self.spin_lock_omega1_squared[ei, si, mi, oi, 
di] = self.spin_lock_omega1[ei, si, mi, oi, di] ** 2
 
@@ -521,7 +521,7 @@
 # Clean the data for all values, which is left over at the end of 
arrays.
 self.back_calc = self.back_calc*self.disp_struct
 
-## For all missing data points, set the back-calculated value to the 
measured values so that it has no effect on the chi-squared value.
+# For all missing data points, set the back-calculated value to the 
measured values so that it has no effect on the chi-squared value.
 if self.has_missing:
 # Replace with values.
 self.back_calc[self.mask_replace_blank.mask] = 
self.values[self.mask_replace_blank.mask]
@@ -554,18 +554,18 @@
 self.r20a_struct[:] = multiply.outer( R20A.reshape(self.NE, self.NS, 
self.NM), self.no_nd_ones )
 self.r20b_struct[:] = multiply.outer( R20B.reshape(self.NE, self.NS, 
self.NM), self.no_nd_ones )
 
-## Back calculate the R2eff values.
+# Back calculate the R2eff values.
 r2eff_CR72(r20a=self.r20a_struct, r20a_orig=R20A, 
r20b=self.r20b_struct, r20b_orig=R20B, pA=pA, dw=self.dw_struct, dw_orig=dw, 
kex=kex, cpmg_frqs=self.cpmg_frqs, back_calc=self.back_calc)
 
 # Clean the data for all values, which is left over at the end of 
arrays.
 self.back_calc = self.back_calc*self.disp_struct
 
-## For all missing data points, set the back-calculated value to the 
measured values so that it has no effect on the chi-squared value.
-if self.has_missing:
-# Replace with values.
-self.back_calc[self.mask_replace_blank.mask] = 
self.values[self.mask_replace_blank.mask]
-
-## Calculate the chi-squared statistic.
+# For all missing data points, set the back-calculated value to the 
measured values so that it has no effect on the chi-squared value.
+if self.has_missing:
+# Replace with values.
+self.back_calc[self.mask_replace_blank.mask] = 
self.values[self.mask_replace_blank.mask]
+
+# Calculate the chi-squared statistic.
 return chi2_rankN(self.values, self.back_calc, self.errors)
 
 
@@ -599,12 +599,12 @@
 # Clean the data for all values, which is left over at the end of 
arrays.
 self.back_calc = self.back_calc*self.disp_struct
 
-## For all missing data points, set the back-calculated value to the 
measured values so that it has no effect on the chi-squared value.
-if self.has_missing:
-# Replace with values.
-self.back_calc[self.mask_replace_blank.mask] = 
self.values[self.mask_replace_blank.mask]
-
-## Calculate the chi-squared statistic.
+# For all missing data points, set the back-calculated value to the 
measured values so that it has no effect on the chi-squared value.
+if self.has_missing:
+# Replace with values.
+self.back_calc[self.mask_replace_blank.mask] = 
self.values[self.mask_replace_blank.mask]
+
+# Calculate the chi-squared statistic.
 return chi2_rankN(self.values

r24076 - /branches/disp_spin_speed/lib/dispersion/

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 10:49:10 2014
New Revision: 24076

URL: http://svn.gna.org/viewcvs/relax?rev=24076view=rev
Log:
Copyright fixes for all the models, where Troels E. Linnet have made changes to 
make them functional for higher dimensional data.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/cr72.py
branches/disp_spin_speed/lib/dispersion/dpl94.py
branches/disp_spin_speed/lib/dispersion/it99.py
branches/disp_spin_speed/lib/dispersion/lm63.py
branches/disp_spin_speed/lib/dispersion/lm63_3site.py
branches/disp_spin_speed/lib/dispersion/m61.py
branches/disp_spin_speed/lib/dispersion/m61b.py
branches/disp_spin_speed/lib/dispersion/mmq_cr72.py
branches/disp_spin_speed/lib/dispersion/mp05.py
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py
branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py
branches/disp_spin_speed/lib/dispersion/tap03.py
branches/disp_spin_speed/lib/dispersion/tp02.py

Modified: branches/disp_spin_speed/lib/dispersion/cr72.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/cr72.py?rev=24076r1=24075r2=24076view=diff
==
--- branches/disp_spin_speed/lib/dispersion/cr72.py (original)
+++ branches/disp_spin_speed/lib/dispersion/cr72.py Wed Jun 18 10:49:10 2014
@@ -2,6 +2,7 @@
 # #
 # Copyright (C) 2009 Sebastien Morin  #
 # Copyright (C) 2013-2014 Edward d'Auvergne   #
+# Copyright (C) 2014 Troels E. Linnet #
 # #
 # This file is part of the program relax (http://www.nmr-relax.com).  #
 # #

Modified: branches/disp_spin_speed/lib/dispersion/dpl94.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/dpl94.py?rev=24076r1=24075r2=24076view=diff
==
--- branches/disp_spin_speed/lib/dispersion/dpl94.py(original)
+++ branches/disp_spin_speed/lib/dispersion/dpl94.pyWed Jun 18 10:49:10 2014
@@ -2,6 +2,7 @@
 # #
 # Copyright (C) 2009 Sebastien Morin  #
 # Copyright (C) 2013-2014 Edward d'Auvergne   #
+# Copyright (C) 2014 Troels E. Linnet #
 # #
 # This file is part of the program relax (http://www.nmr-relax.com).  #
 # #

Modified: branches/disp_spin_speed/lib/dispersion/it99.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/it99.py?rev=24076r1=24075r2=24076view=diff
==
--- branches/disp_spin_speed/lib/dispersion/it99.py (original)
+++ branches/disp_spin_speed/lib/dispersion/it99.py Wed Jun 18 10:49:10 2014
@@ -2,6 +2,7 @@
 # #
 # Copyright (C) 2009 Sebastien Morin  #
 # Copyright (C) 2013-2014 Edward d'Auvergne   #
+# Copyright (C) 2014 Troels E. Linnet #
 # #
 # This file is part of the program relax (http://www.nmr-relax.com).  #
 # #

Modified: branches/disp_spin_speed/lib/dispersion/lm63.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/lm63.py?rev=24076r1=24075r2=24076view=diff
==
--- branches/disp_spin_speed/lib/dispersion/lm63.py (original)
+++ branches/disp_spin_speed/lib/dispersion/lm63.py Wed Jun 18 10:49:10 2014
@@ -2,6 +2,7 @@
 # #
 # Copyright (C) 2009 Sebastien Morin  #
 # Copyright (C) 2013-2014 Edward

r24077 - /branches/disp_spin_speed/lib/dispersion/tsmfk01.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 10:50:36 2014
New Revision: 24077

URL: http://svn.gna.org/viewcvs/relax?rev=24077view=rev
Log:
Copyright fix for model TSMFK01.

Sebastien Morin did not take part of implementing the TSMK01 modelÃ.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/tsmfk01.py

Modified: branches/disp_spin_speed/lib/dispersion/tsmfk01.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/tsmfk01.py?rev=24077r1=24076r2=24077view=diff
==
--- branches/disp_spin_speed/lib/dispersion/tsmfk01.py  (original)
+++ branches/disp_spin_speed/lib/dispersion/tsmfk01.py  Wed Jun 18 10:50:36 2014
@@ -1,6 +1,5 @@
 ###
 # #
-# Copyright (C) 2009 Sebastien Morin  #
 # Copyright (C) 2013-2014 Edward d'Auvergne   #
 # Copyright (C) 2013 Troels E. Linnet #
 # #


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r24081 - /branches/disp_spin_speed/specific_analyses/relax_disp/optimisation.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 11:37:12 2014
New Revision: 24081

URL: http://svn.gna.org/viewcvs/relax?rev=24081view=rev
Log:
Made the processor.return_object get the back_calc structure in the expected 
order.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/specific_analyses/relax_disp/optimisation.py

Modified: branches/disp_spin_speed/specific_analyses/relax_disp/optimisation.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/specific_analyses/relax_disp/optimisation.py?rev=24081r1=24080r2=24081view=diff
==
--- branches/disp_spin_speed/specific_analyses/relax_disp/optimisation.py   
(original)
+++ branches/disp_spin_speed/specific_analyses/relax_disp/optimisation.py   
Wed Jun 18 11:37:12 2014
@@ -770,7 +770,7 @@
 print(Simulation %s, cluster %s % (self.sim_index+1, 
self.spin_ids))
 
 # Create the result command object to send back to the master.
-processor.return_object(Disp_result_command(processor=processor, 
memo_id=self.memo_id, param_vector=param_vector, chi2=chi2, 
iter_count=iter_count, f_count=f_count, g_count=g_count, h_count=h_count, 
warning=warning, missing=self.missing, back_calc=model.back_calc, 
completed=False))
+processor.return_object(Disp_result_command(processor=processor, 
memo_id=self.memo_id, param_vector=param_vector, chi2=chi2, 
iter_count=iter_count, f_count=f_count, g_count=g_count, h_count=h_count, 
warning=warning, missing=self.missing, back_calc=model.get_back_calc(), 
completed=False))
 
 
 


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r24083 - in /branches/disp_spin_speed: ./ test_suite/verification_tests/library.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 11:46:33 2014
New Revision: 24083

URL: http://svn.gna.org/viewcvs/relax?rev=24083view=rev
Log:
Merged revisions 24058 via svnmerge from 
svn+ssh://tlin...@svn.gna.org/svn/relax/trunk


  r24058 | bugman | 2014-06-17 19:46:10 +0200 (Tue, 17 Jun 2014) | 6 lines
  
  Fix for the Library.test_library_independence verification test on MS Windows.
  
  The tearDown() method now uses the error handling 
test_suite.clean_up.deletion() function to remove
  the copied version of the relax library.


Modified:
branches/disp_spin_speed/   (props changed)
branches/disp_spin_speed/test_suite/verification_tests/library.py

Propchange: branches/disp_spin_speed/
--
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Jun 18 11:46:33 2014
@@ -1 +1 @@
-/trunk:1-24051
+/trunk:1-24082

Modified: branches/disp_spin_speed/test_suite/verification_tests/library.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/verification_tests/library.py?rev=24083r1=24082r2=24083view=diff
==
--- branches/disp_spin_speed/test_suite/verification_tests/library.py   
(original)
+++ branches/disp_spin_speed/test_suite/verification_tests/library.py   Wed Jun 
18 11:46:33 2014
@@ -32,6 +32,7 @@
 
 # relax module imports.
 from status import Status; status = Status()
+from test_suite.clean_up import deletion
 
 
 class Library(TestCase):
@@ -48,7 +49,7 @@
 Clean up after the library tests.
 
 # Remove the temporary directory and all its contents.
-rmtree(self.tmpdir)
+deletion(obj=self, name='tmpdir', dir=True)
 
 
 def test_library_independence(self):


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r24091 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 15:44:58 2014
New Revision: 24091

URL: http://svn.gna.org/viewcvs/relax?rev=24091view=rev
Log:
Added DPL94 profiling script.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py

[This mail would be too long, it was shortened to contain the URLs only.]

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py?rev=24091r1=24090r2=24091view=diff


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r24092 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 15:58:31 2014
New Revision: 24092

URL: http://svn.gna.org/viewcvs/relax?rev=24092view=rev
Log:
Modified profiling script for TSMK01, to use correct parameters k_AB and r20a.

Or else, the lib functions is just calculating with zero?

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py?rev=24092r1=24091r2=24092view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py
   (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tsmfk01.py
   Wed Jun 18 15:58:31 2014
@@ -110,7 +110,7 @@
 Class Profile inherits the Dispersion container class object.
 
 
-def __init__(self, num_spins=1, model=None, r2=None, r2a=None, r2b=None, 
dw=None, pA=None, kex=None, spins_params=None):
+def __init__(self, num_spins=1, model=None, r2=None, r2a=None, r2b=None, 
dw=None, pA=None, kex=None, k_AB=None, spins_params=None):
 
 Special method __init__() is called first (acts as Constructor).
 It brings in data from outside the class like the variable num_spins.
@@ -136,6 +136,8 @@
 @type pA:   float
 @keyword kex:   The rate of exchange.
 @type kex:  float
+@keyword k_AB:  The exchange rate from state A to state B
+@type k_AB: float
 @keyword spins_params:  List of parameter strings used in dispersion 
model.
 @type spins_params: array of strings
 
@@ -172,7 +174,7 @@
 self.error.append([1.0]*len(cpmg_point))
 
 # Assemble param vector.
-self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b, 
dw=dw, pA=pA, kex=kex, spins_params=spins_params)
+self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b, 
dw=dw, pA=pA, kex=kex, k_AB=k_AB, spins_params=spins_params)
 
 # Make nested list arrays of data. And return them.
 values, errors, cpmg_frqs, missing, frqs, exp_types, relax_times, 
offsets = self.return_r2eff_arrays()
@@ -316,7 +318,7 @@
 return values, errors, cpmg_frqs, missing, frqs, exp_types, 
relax_times, offsets
 
 
-def assemble_param_vector(self, r2=None, r2a=None, r2b=None, dw=None, 
pA=None, kex=None, spins_params=None):
+def assemble_param_vector(self, r2=None, r2a=None, r2b=None, dw=None, 
pA=None, kex=None, k_AB=None, spins_params=None):
 Assemble the dispersion relaxation dispersion curve fitting 
parameter vector.
 
 @keyword r2:The transversal relaxation rate.
@@ -331,6 +333,8 @@
 @type pA:   float
 @keyword kex:   The rate of exchange.
 @type kex:  float
+@keyword k_AB:  The exchange rate from state A to state B
+@type k_AB: float
 @keyword spins_params:  List of parameter strings used in dispersion 
model.
 @type spins_params: array of strings
 @return:An array of the parameter values of the 
dispersion relaxation model.
@@ -357,6 +361,8 @@
 value = pA
 elif param_name == 'kex':
 value = kex
+elif param_name == 'k_AB':
+value = k_AB
 
 # Add to the vector.
 param_vector.append(value)
@@ -411,6 +417,8 @@
 yield 'pA', 0, 0
 elif param == 'kex':
 yield 'kex', 0, 0
+elif param == 'k_AB':
+yield 'k_AB', 0, 0
 
 
 def calc(self, params):
@@ -441,7 +449,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, dw=3.0, k_AB=10.0, 
spins_params=['r2a', 'dw', 'k_AB'])
 
 # Loop 100 times for each spin in the clustered analysis (to make the 
timing numbers equivalent).
 for spin_index in xrange(100):
@@ -465,7 +473,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, dw=3.0, k_AB=10.0, 
spins_params=['r2a', 'dw', 'k_AB'])
 
 # Repeat the function call, to simulate minimisation.
 for i in xrange(iter):
@@ -476,38 +484,3 @@
 # Execute main function.
 if __name__

r24093 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 16:03:46 2014
New Revision: 24093

URL: http://svn.gna.org/viewcvs/relax?rev=24093view=rev
Log:
Changes to profiling script of ns_cpmg_2site_expanded.

The model does not have r20a and r20b, but only r2.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py?rev=24093r1=24092r2=24093view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py
(original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py
Wed Jun 18 16:03:46 2014
@@ -442,7 +442,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Loop 100 times for each spin in the clustered analysis (to make the 
timing numbers equivalent).
 for spin_index in xrange(100):
@@ -466,7 +466,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Repeat the function call, to simulate minimisation.
 for i in xrange(iter):
@@ -477,38 +477,3 @@
 # Execute main function.
 if __name__ == __main__:
 main()
-
-def test_reshape():
-C1 = Profile(num_spins=1, model=MODEL_NS_CPMG_2SITE_EXPANDED, r2a=5.0, 
r2b=10.0, dw=3.0, pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 
'kex'])
-end_index = C1.model.end_index
-#print(end_index:, end_index)
-num_spins = C1.model.num_spins
-#print(num_spins:, num_spins)
-num_frq = C1.model.num_frq
-#print(num_frq:, num_frq)
-params = C1.params
-#print(params, params)
-
-R20 = params[:end_index[1]].reshape(num_spins*2, num_frq)
-R20A = R20[::2].flatten()
-R20B = R20[1::2].flatten()
-dw = params[end_index[1]:end_index[2]]
-pA = params[end_index[2]]
-kex = params[end_index[2]+1]
-print(R20A, R20A, len(R20A))
-print(R20B, R20B, len(R20B))
-print(dw, dw, len(dw))
-print(dw, pA)
-print(kex, kex)
-
-for si in range(num_spins):
-for mi in range(num_frq):
-r20_index = mi + si*num_frq
-r20a=R20A[r20_index]
-r20b=R20B[r20_index]
-print(r20a, r20a, r20b, r20b)
-
-model = C1.calc(params)
-print(model)
-
-#test_reshape()


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r24094 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 16:07:10 2014
New Revision: 24094

URL: http://svn.gna.org/viewcvs/relax?rev=24094view=rev
Log:
Made changes to the profiling script of NS_CPMG_2SITE_3D.

Need to use the full model, when r2a and r2b is specified.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py?rev=24094r1=24093r2=24094view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
  (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
  Wed Jun 18 16:07:10 2014
@@ -424,7 +424,7 @@
 
 
 # Return chi2 value.
-chi2 = self.model.func_ns_cpmg_2site_3D(params)
+chi2 = self.model.func_ns_cpmg_2site_3D_full(params)
 return chi2
 
 


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r24095 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 16:17:42 2014
New Revision: 24095

URL: http://svn.gna.org/viewcvs/relax?rev=24095view=rev
Log:
Changes to profiling script of ns expanded.

The unpacking can be removed.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py?rev=24095r1=24094r2=24095view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py
(original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_expanded.py
Wed Jun 18 16:17:42 2014
@@ -184,23 +184,6 @@
 @rtype: lists of numpy float arrays, lists of numpy float 
arrays, lists of numpy float arrays, numpy rank-2 int array
 
 
-# Unpack the parameter values.
-# Initialise the post spin parameter indices.
-end_index = []
-# The spin and frequency dependent R2 parameters.
-end_index.append(len(self.exp_type) * self.num_spins * 
len(self.fields))
-if self.model in [MODEL_B14_FULL, MODEL_NS_CPMG_2SITE_EXPANDED, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
-end_index.append(2 * len(self.exp_type) * self.num_spins * 
len(self.fields))
-# The spin and dependent parameters (phi_ex, dw, padw2).
-end_index.append(end_index[-1] + self.num_spins)
-
-# Unpack the parameter values.
-R20 = self.params[:end_index[1]].reshape(self.num_spins*2, 
len(self.fields))
-R20A = R20[::2].flatten()
-R20B = R20[1::2].flatten()
-dw = self.params[end_index[1]:end_index[2]]
-pA = self.params[end_index[2]]
-kex = self.params[end_index[2]+1]
 
 # Initialise the data structures for the target function.
 exp_types = []
@@ -273,12 +256,7 @@
 cpmg_frqs[ei][mi][oi] = self.points[mi]
 
 # Calculate how the value should be, so chi2 gets zero.
-# The R20 index.
-r20_index = mi + si*len(self.fields)
-# Convert dw from ppm to rad/s.
-dw_frq = dw[si] * frqs[ei][si][mi]
-r20a=R20A[r20_index]
-r20b=R20B[r20_index]
+
 back_calc = array([0.0]*len(cpmg_frqs[ei][mi][oi]))
 
 for oi in range(len(self.offset)):
@@ -466,7 +444,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Repeat the function call, to simulate minimisation.
 for i in xrange(iter):


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r24096 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 16:33:46 2014
New Revision: 24096

URL: http://svn.gna.org/viewcvs/relax?rev=24096view=rev
Log:
Fix for the profiling script of NS cpmg 3D.

The model should also be speciffied to full.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py?rev=24096r1=24095r2=24096view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
  (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
  Wed Jun 18 16:33:46 2014
@@ -183,24 +183,6 @@
 @return:The numpy array structures of the R2eff/R1rho values, 
errors, missing data, and corresponding Larmor frequencies.  For each 
structure, the first dimension corresponds to the experiment types, the second 
the spins of a spin block, the third to the spectrometer field strength, and 
the fourth is the dispersion points.  For the Larmor frequency structure, the 
fourth dimension is omitted.  For R1rho-type data, an offset dimension is 
inserted between the spectrometer field strength and the dispersion points.
 @rtype: lists of numpy float arrays, lists of numpy float 
arrays, lists of numpy float arrays, numpy rank-2 int array
 
-
-# Unpack the parameter values.
-# Initialise the post spin parameter indices.
-end_index = []
-# The spin and frequency dependent R2 parameters.
-end_index.append(len(self.exp_type) * self.num_spins * 
len(self.fields))
-if self.model in [MODEL_B14_FULL, MODEL_NS_CPMG_2SITE_3D, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
-end_index.append(2 * len(self.exp_type) * self.num_spins * 
len(self.fields))
-# The spin and dependent parameters (phi_ex, dw, padw2).
-end_index.append(end_index[-1] + self.num_spins)
-
-# Unpack the parameter values.
-R20 = self.params[:end_index[1]].reshape(self.num_spins*2, 
len(self.fields))
-R20A = R20[::2].flatten()
-R20B = R20[1::2].flatten()
-dw = self.params[end_index[1]:end_index[2]]
-pA = self.params[end_index[2]]
-kex = self.params[end_index[2]+1]
 
 # Initialise the data structures for the target function.
 exp_types = []
@@ -273,12 +255,6 @@
 cpmg_frqs[ei][mi][oi] = self.points[mi]
 
 # Calculate how the value should be, so chi2 gets zero.
-# The R20 index.
-r20_index = mi + si*len(self.fields)
-# Convert dw from ppm to rad/s.
-dw_frq = dw[si] * frqs[ei][si][mi]
-r20a=R20A[r20_index]
-r20b=R20B[r20_index]
 back_calc = array([0.0]*len(cpmg_frqs[ei][mi][oi]))
 
 for oi in range(len(self.offset)):
@@ -428,7 +404,7 @@
 return chi2
 
 
-def single(num_spins=1, model=MODEL_NS_CPMG_2SITE_3D, iter=None):
+def single(num_spins=1, model=MODEL_NS_CPMG_2SITE_3D_FULL, iter=None):
 Calculate for a single spin.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -452,7 +428,7 @@
 print(chi2 single:, chi2)
 
 
-def cluster(num_spins=100, model=MODEL_NS_CPMG_2SITE_3D, iter=None):
+def cluster(num_spins=100, model=MODEL_NS_CPMG_2SITE_3D_FULL, iter=None):
 Calculate for a number of clustered spins.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -476,39 +452,4 @@
 
 # Execute main function.
 if __name__ == __main__:
-main()
-
-def test_reshape():
-C1 = Profile(num_spins=1, model=MODEL_NS_CPMG_2SITE_3D, r2a=5.0, r2b=10.0, 
dw=3.0, pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
-end_index = C1.model.end_index
-#print(end_index:, end_index)
-num_spins = C1.model.num_spins
-#print(num_spins:, num_spins)
-num_frq = C1.model.num_frq
-#print(num_frq:, num_frq)
-params = C1.params
-#print(params, params)
-
-R20 = params[:end_index[1]].reshape(num_spins*2, num_frq)
-R20A = R20[::2].flatten()
-R20B = R20[1::2].flatten()
-dw = params[end_index[1]:end_index[2]]
-pA = params[end_index[2]]
-kex = params[end_index[2]+1]
-print(R20A, R20A, len(R20A))
-print(R20B, R20B, len(R20B))
-print(dw, dw, len(dw))
-print(dw, pA)
-print(kex, kex)
-
-for si in range(num_spins):
-for mi in range(num_frq):
-r20_index = mi + si*num_frq
-r20a=R20A

r24098 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_2site.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 16:44:12 2014
New Revision: 24098

URL: http://svn.gna.org/viewcvs/relax?rev=24098view=rev
Log:
Copied profiling script of DPL94 to ns r1rho 2site.


Added:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_2site.py
  - copied unchanged from r24097, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py


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r24100 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_2site.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 16:48:50 2014
New Revision: 24100

URL: http://svn.gna.org/viewcvs/relax?rev=24100view=rev
Log:
Added profiling script for NS R1rho 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_2site.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_2site.py?rev=24100r1=24099r2=24100view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_2site.py
(original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_r1rho_2site.py
Wed Jun 18 16:48:50 2014
@@ -63,7 +63,7 @@
 def main():
 if True:
 # Nr of iterations.
-nr_iter = 1000
+nr_iter = 10
 
 # Print statistics.
 verbose = True
@@ -523,11 +523,11 @@
 
 
 # Return chi2 value.
-chi2 = self.model.func_DPL94(params)
+chi2 = self.model.func_ns_r1rho_2site(params)
 return chi2
 
 
-def single(num_spins=1, model=MODEL_DPL94, iter=None):
+def single(num_spins=1, model=MODEL_NS_R1RHO_2SITE, iter=None):
 Calculate for a single spin.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -541,7 +541,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2=5.0, phi_ex=1.0, 
kex=5000.0, spins_params=['r2', 'phi_ex', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=1.0, pA=0.9, 
kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Loop 100 times for each spin in the clustered analysis (to make the 
timing numbers equivalent).
 for spin_index in xrange(100):
@@ -551,7 +551,7 @@
 print(chi2 single:, chi2)
 
 
-def cluster(num_spins=100, model=MODEL_DPL94, iter=None):
+def cluster(num_spins=100, model=MODEL_NS_R1RHO_2SITE, iter=None):
 Calculate for a number of clustered spins.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -565,7 +565,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2=5.0, phi_ex=1.0, 
kex=5000.0, spins_params=['r2', 'phi_ex', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=1.0, pA=0.9, 
kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Repeat the function call, to simulate minimisation.
 for i in xrange(iter):


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r24103 - in /branches/disp_spin_speed: lib/dispersion/lm63_3site.py target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 17:11:24 2014
New Revision: 24103

URL: http://svn.gna.org/viewcvs/relax?rev=24103view=rev
Log:
Moved the Ãparter conversion in LM63 3site into the lib function.

This cleans up the target api function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/lm63_3site.py
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/lib/dispersion/lm63_3site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/lm63_3site.py?rev=24103r1=24102r2=24103view=diff
==
--- branches/disp_spin_speed/lib/dispersion/lm63_3site.py   (original)
+++ branches/disp_spin_speed/lib/dispersion/lm63_3site.py   Wed Jun 18 
17:11:24 2014
@@ -69,7 +69,7 @@
 from numpy.ma import fix_invalid, masked_where
 
 
-def r2eff_LM63_3site(r20=None, rex_B=None, rex_C=None, quart_kB=None, 
quart_kC=None, cpmg_frqs=None, back_calc=None):
+def r2eff_LM63_3site(r20=None, phi_ex_B=None, phi_ex_C=None, kB=None, kC=None, 
cpmg_frqs=None, back_calc=None):
 Calculate the R2eff values for the LM63 3-site model.
 
 See the module docstring for details.
@@ -77,19 +77,29 @@
 
 @keyword r20:   The R20 parameter value (R2 with no exchange).
 @type r20:  numpy float array of rank [NS][NM][NO][ND]
-@keyword rex_B: The phi_ex_B / kB parameter value.
-@type rex_B:numpy float array of rank [NS][NM][NO][ND]
-@keyword rex_C: The phi_ex_C / kC parameter value.
-@type rex_C:numpy float array of rank [NE][NS][NM][NO][ND]
-@keyword quart_kB:  Approximate chemical exchange rate constant 
between sites A and B (the exchange rate in rad/s) divided by 4.
-@type quart_kB: float
-@keyword quart_kC:  Approximate chemical exchange rate constant 
between sites A and C (the exchange rate in rad/s) divided by 4.
-@type quart_kC: float
+@keyword phi_ex_B:  The fast exchange factor between sites A and B 
(ppm^2)
+@type phi_ex_B: numpy float array of rank [NS][NM][NO][ND]
+@keyword phi_ex_C:  The fast exchange factor between sites A and C 
(ppm^2)
+@type phi_ex_C: numpy float array of rank [NE][NS][NM][NO][ND]
+@keyword kB:Approximate chemical exchange rate constant 
between sites A and B (the exchange rate in rad/s).
+@type kB:   float
+@keyword kC:Approximate chemical exchange rate constant 
between sites A and C (the exchange rate in rad/s).
+@type kC:   float
 @keyword cpmg_frqs: The CPMG nu1 frequencies.
 @type cpmg_frqs:numpy float array of rank [NE][NS][NM][NO][ND]
 @keyword back_calc: The array for holding the back calculated R2eff 
values.  Each element corresponds to one of the CPMG nu1 frequencies.
 @type back_calc:numpy float array of rank [NE][NS][NM][NO][ND]
 
+
+# Once off parameter conversions.
+# The phi_ex_B / kB parameter value.
+rex_B = phi_ex_B / kB
+# The phi_ex_C / kC parameter value.
+rex_C = phi_ex_C / kC
+# Approximate chemical exchange rate constant between sites A and B (the 
exchange rate in rad/s) divided by 4.
+quart_kB = kB / 4.0
+# Approximate chemical exchange rate constant between sites A and C (the 
exchange rate in rad/s) divided by 4.
+quart_kC = kC / 4.0
 
 # Flag to tell if values should be replaced.
 t_rex_zero = False

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24103r1=24102r2=24103view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Wed Jun 18 
17:11:24 2014
@@ -1062,21 +1062,15 @@
 kB = params[self.end_index[2]]
 kC = params[self.end_index[2]+1]
 
-# Once off parameter conversions.
-rex_B = phi_ex_B / kB
-rex_C = phi_ex_C / kC
-quart_kB = kB / 4.0
-quart_kC = kC / 4.0
-
 # Convert phi_ex (or rex) from ppm^2 to (rad/s)^2.
-multiply( multiply.outer( rex_B.reshape(1, self.NS), 
self.nm_no_nd_ones ), self.frqs_squared, out=self.phi_ex_B_struct )
-multiply( multiply.outer( rex_C.reshape(1, self.NS), 
self.nm_no_nd_ones ), self.frqs_squared, out=self.phi_ex_C_struct )
+multiply( multiply.outer( phi_ex_B.reshape(1, self.NS), 
self.nm_no_nd_ones ), self.frqs_squared, out=self.phi_ex_B_struct )
+multiply( multiply.outer( phi_ex_C.reshape(1, self.NS), 
self.nm_no_nd_ones ), self.frqs_squared, out=self.phi_ex_C_struct )
 
 # Reshape R20 to per experiment

r24104 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tap03.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 17:12:50 2014
New Revision: 24104

URL: http://svn.gna.org/viewcvs/relax?rev=24104view=rev
Log:
Copied profiling script for DPL94 to TAP03.


Added:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tap03.py
  - copied unchanged from r24097, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py


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r24105 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tp02.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 17:13:47 2014
New Revision: 24105

URL: http://svn.gna.org/viewcvs/relax?rev=24105view=rev
Log:
Copied profiling script for DPL94 to TP02.

Added:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tp02.py
  - copied unchanged from r24097, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py


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r24106 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_mp05.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 17:15:27 2014
New Revision: 24106

URL: http://svn.gna.org/viewcvs/relax?rev=24106view=rev
Log:
Copied profiling script for DPL94 to MP05.

Added:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_mp05.py
  - copied unchanged from r24097, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py


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r24107 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_m61.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 17:16:24 2014
New Revision: 24107

URL: http://svn.gna.org/viewcvs/relax?rev=24107view=rev
Log:
Copied profiling script for DPL94 to M61.

Added:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_m61.py
  - copied unchanged from r24097, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_dpl94.py


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r24108 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tap03.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 17:21:39 2014
New Revision: 24108

URL: http://svn.gna.org/viewcvs/relax?rev=24108view=rev
Log:
Modified profiling script for TAP03 to be used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tap03.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tap03.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tap03.py?rev=24108r1=24107r2=24108view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tap03.py
 (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tap03.py
 Wed Jun 18 17:21:39 2014
@@ -63,7 +63,7 @@
 def main():
 if True:
 # Nr of iterations.
-nr_iter = 1000
+nr_iter = 10
 
 # Print statistics.
 verbose = True
@@ -523,11 +523,11 @@
 
 
 # Return chi2 value.
-chi2 = self.model.func_DPL94(params)
+chi2 = self.model.func_TAP03(params)
 return chi2
 
 
-def single(num_spins=1, model=MODEL_DPL94, iter=None):
+def single(num_spins=1, model=MODEL_TAP03, iter=None):
 Calculate for a single spin.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -541,7 +541,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2=5.0, phi_ex=1.0, 
kex=5000.0, spins_params=['r2', 'phi_ex', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=1.0, pA=0.9, 
kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Loop 100 times for each spin in the clustered analysis (to make the 
timing numbers equivalent).
 for spin_index in xrange(100):
@@ -551,7 +551,7 @@
 print(chi2 single:, chi2)
 
 
-def cluster(num_spins=100, model=MODEL_DPL94, iter=None):
+def cluster(num_spins=100, model=MODEL_TAP03, iter=None):
 Calculate for a number of clustered spins.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -565,7 +565,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2=5.0, phi_ex=1.0, 
kex=5000.0, spins_params=['r2', 'phi_ex', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=1.0, pA=0.9, 
kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Repeat the function call, to simulate minimisation.
 for i in xrange(iter):


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r24109 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tp02.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 17:23:44 2014
New Revision: 24109

URL: http://svn.gna.org/viewcvs/relax?rev=24109view=rev
Log:
Modified profiling script for TP02, to be used.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tp02.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tp02.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tp02.py?rev=24109r1=24108r2=24109view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tp02.py
  (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_tp02.py
  Wed Jun 18 17:23:44 2014
@@ -63,7 +63,7 @@
 def main():
 if True:
 # Nr of iterations.
-nr_iter = 1000
+nr_iter = 10
 
 # Print statistics.
 verbose = True
@@ -523,11 +523,11 @@
 
 
 # Return chi2 value.
-chi2 = self.model.func_DPL94(params)
+chi2 = self.model.func_TP02(params)
 return chi2
 
 
-def single(num_spins=1, model=MODEL_DPL94, iter=None):
+def single(num_spins=1, model=MODEL_TP02, iter=None):
 Calculate for a single spin.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -541,7 +541,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2=5.0, phi_ex=1.0, 
kex=5000.0, spins_params=['r2', 'phi_ex', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=1.0, pA=0.9, 
kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Loop 100 times for each spin in the clustered analysis (to make the 
timing numbers equivalent).
 for spin_index in xrange(100):
@@ -551,7 +551,7 @@
 print(chi2 single:, chi2)
 
 
-def cluster(num_spins=100, model=MODEL_DPL94, iter=None):
+def cluster(num_spins=100, model=MODEL_TP02, iter=None):
 Calculate for a number of clustered spins.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -565,7 +565,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2=5.0, phi_ex=1.0, 
kex=5000.0, spins_params=['r2', 'phi_ex', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=1.0, pA=0.9, 
kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Repeat the function call, to simulate minimisation.
 for i in xrange(iter):


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r24110 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_mp05.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 17:27:54 2014
New Revision: 24110

URL: http://svn.gna.org/viewcvs/relax?rev=24110view=rev
Log:
Modified profiling script for MP05.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_mp05.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_mp05.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_mp05.py?rev=24110r1=24109r2=24110view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_mp05.py
  (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_mp05.py
  Wed Jun 18 17:27:54 2014
@@ -63,7 +63,7 @@
 def main():
 if True:
 # Nr of iterations.
-nr_iter = 1000
+nr_iter = 10
 
 # Print statistics.
 verbose = True
@@ -523,11 +523,11 @@
 
 
 # Return chi2 value.
-chi2 = self.model.func_DPL94(params)
+chi2 = self.model.func_MP05(params)
 return chi2
 
 
-def single(num_spins=1, model=MODEL_DPL94, iter=None):
+def single(num_spins=1, model=MODEL_MP05, iter=None):
 Calculate for a single spin.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -541,7 +541,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2=5.0, phi_ex=1.0, 
kex=5000.0, spins_params=['r2', 'phi_ex', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=1.0, pA=0.9, 
kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Loop 100 times for each spin in the clustered analysis (to make the 
timing numbers equivalent).
 for spin_index in xrange(100):
@@ -551,7 +551,7 @@
 print(chi2 single:, chi2)
 
 
-def cluster(num_spins=100, model=MODEL_DPL94, iter=None):
+def cluster(num_spins=100, model=MODEL_MP05, iter=None):
 Calculate for a number of clustered spins.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -565,7 +565,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2=5.0, phi_ex=1.0, 
kex=5000.0, spins_params=['r2', 'phi_ex', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=1.0, pA=0.9, 
kex=5000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Repeat the function call, to simulate minimisation.
 for i in xrange(iter):


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r24111 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_m61.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 17:31:55 2014
New Revision: 24111

URL: http://svn.gna.org/viewcvs/relax?rev=24111view=rev
Log:
Modified profiling script for M61.

This is the last one.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_m61.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_m61.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_m61.py?rev=24111r1=24110r2=24111view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_m61.py
   (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_m61.py
   Wed Jun 18 17:31:55 2014
@@ -63,7 +63,7 @@
 def main():
 if True:
 # Nr of iterations.
-nr_iter = 1000
+nr_iter = 100
 
 # Print statistics.
 verbose = True
@@ -523,11 +523,11 @@
 
 
 # Return chi2 value.
-chi2 = self.model.func_DPL94(params)
+chi2 = self.model.func_M61(params)
 return chi2
 
 
-def single(num_spins=1, model=MODEL_DPL94, iter=None):
+def single(num_spins=1, model=MODEL_M61, iter=None):
 Calculate for a single spin.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -551,7 +551,7 @@
 print(chi2 single:, chi2)
 
 
-def cluster(num_spins=100, model=MODEL_DPL94, iter=None):
+def cluster(num_spins=100, model=MODEL_M61, iter=None):
 Calculate for a number of clustered spins.
 
 @keyword num_spins: Number of spins in the cluster.


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r24113 - in /branches/disp_spin_speed: lib/dispersion/mmq_cr72.py target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 17:39:08 2014
New Revision: 24113

URL: http://svn.gna.org/viewcvs/relax?rev=24113view=rev
Log:
Moved the parameter conversion of MMQ CR72 into lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/mmq_cr72.py
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/lib/dispersion/mmq_cr72.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/mmq_cr72.py?rev=24113r1=24112r2=24113view=diff
==
--- branches/disp_spin_speed/lib/dispersion/mmq_cr72.py (original)
+++ branches/disp_spin_speed/lib/dispersion/mmq_cr72.py Wed Jun 18 17:39:08 2014
@@ -52,7 +52,7 @@
 from numpy.ma import fix_invalid, masked_greater_equal, masked_where
 
 
-def r2eff_mmq_cr72(r20=None, pA=None, pB=None, dw=None, dwH=None, kex=None, 
k_AB=None, k_BA=None, cpmg_frqs=None, inv_tcpmg=None, tcp=None, back_calc=None):
+def r2eff_mmq_cr72(r20=None, pA=None, dw=None, dwH=None, kex=None, 
cpmg_frqs=None, inv_tcpmg=None, tcp=None, back_calc=None):
 The CR72 model extended to MMQ CPMG data.
 
 This function calculates and stores the R2eff values.
@@ -62,18 +62,12 @@
 @type r20:  numpy float array of rank [NS][NM][NO][ND]
 @keyword pA:The population of state A.
 @type pA:   float
-@keyword pB:The population of state B.
-@type pB:   float
 @keyword dw:The chemical exchange difference between states A 
and B in rad/s.
 @type dw:   numpy float array of rank [NS][NM][NO][ND]
 @keyword dwH:   The proton chemical exchange difference between 
states A and B in rad/s.
 @type dwH:  numpy float array of rank [NS][NM][NO][ND]
 @keyword kex:   The kex parameter value (the exchange rate in 
rad/s).
 @type kex:  float
-@keyword k_AB:  The rate of exchange from site A to B (rad/s).
-@type k_AB: float
-@keyword k_BA:  The rate of exchange from site B to A (rad/s).
-@type k_BA: float
 @keyword cpmg_frqs: The CPMG nu1 frequencies.
 @type cpmg_frqs:numpy float array of rank [NS][NM][NO][ND]
 @keyword inv_tcpmg: The inverse of the total duration of the CPMG 
element (in inverse seconds).
@@ -83,6 +77,11 @@
 @keyword back_calc: The array for holding the back calculated R2eff 
values.  Each element corresponds to one of the CPMG nu1 frequencies.
 @type back_calc:numpy float array of rank [NS][NM][NO][ND]
 
+
+# Once off parameter conversions.
+pB = 1.0 - pA
+k_BA = pA * kex
+k_AB = pB * kex
 
 # Flag to tell if values should be replaced if max_etapos in cosh function 
is violated.
 t_dw_dw_H_zero = False

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24113r1=24112r2=24113view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Wed Jun 18 
17:39:08 2014
@@ -1261,11 +1261,6 @@
 pA = params[self.end_index[2]]
 kex = params[self.end_index[2]+1]
 
-# Once off parameter conversions.
-pB = 1.0 - pA
-k_BA = pA * kex
-k_AB = pB * kex
-
 # Convert dw and dwH from ppm to rad/s. Use the out argument, to pass 
directly to structure.
 multiply( multiply.outer( dw.reshape(1, self.NS), self.nm_no_nd_ones 
), self.frqs, out=self.dw_struct )
 multiply( multiply.outer( dwH.reshape(1, self.NS), self.nm_no_nd_ones 
), self.frqs_H, out=self.dwH_struct )
@@ -1298,7 +1293,7 @@
 aliased_dwH = dw_frq
 
 # Back calculate the R2eff values.
-r2eff_mmq_cr72(r20=r20, pA=pA, pB=pB, dw=aliased_dw, 
dwH=aliased_dwH, kex=kex, k_AB=k_AB, k_BA=k_BA, cpmg_frqs=self.cpmg_frqs[ei], 
inv_tcpmg=self.inv_relax_times[ei], tcp=self.tau_cpmg[ei], 
back_calc=self.back_calc[ei])
+r2eff_mmq_cr72(r20=r20, pA=pA, dw=aliased_dw, dwH=aliased_dwH, 
kex=kex, cpmg_frqs=self.cpmg_frqs[ei], inv_tcpmg=self.inv_relax_times[ei], 
tcp=self.tau_cpmg[ei], back_calc=self.back_calc[ei])
 
 # Clean the data for all values, which is left over at the end of 
arrays.
 self.back_calc = self.back_calc*self.disp_struct


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r24114 - in /branches/disp_spin_speed: lib/dispersion/ns_mmq_2site.py target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 17:52:07 2014
New Revision: 24114

URL: http://svn.gna.org/viewcvs/relax?rev=24114view=rev
Log:
Moved the paramter conversions of k_AB, k_BA and pB into lib function of NS MMQ 
2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py?rev=24114r1=24113r2=24114view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py Wed Jun 18 
17:52:07 2014
@@ -83,7 +83,7 @@
 matrix[1, 1] = -k_BA + 1.j*dw - R20B
 
 
-def r2eff_ns_mmq_2site_mq(M0=None, F_vector=array([1, 0], float64), m1=None, 
m2=None, R20A=None, R20B=None, pA=None, pB=None, dw=None, dwH=None, k_AB=None, 
k_BA=None, inv_tcpmg=None, tcp=None, back_calc=None, num_points=None, 
power=None):
+def r2eff_ns_mmq_2site_mq(M0=None, F_vector=array([1, 0], float64), m1=None, 
m2=None, R20A=None, R20B=None, pA=None, dw=None, dwH=None, kex=None, 
inv_tcpmg=None, tcp=None, back_calc=None, num_points=None, power=None):
 The 2-site numerical solution to the Bloch-McConnell equation for MQ 
data.
 
 The notation used here comes from:
@@ -111,16 +111,12 @@
 @type R20B: numpy float array of rank [NS][NM][NO][ND]
 @keyword pA:The population of state A.
 @type pA:   float
-@keyword pB:The population of state B.
-@type pB:   float
 @keyword dw:The chemical exchange difference between states A 
and B in rad/s.
 @type dw:   numpy float array of rank [NS][NM][NO][ND]
 @keyword dwH:   The proton chemical exchange difference between 
states A and B in rad/s.
 @type dwH:  numpy float array of rank [NS][NM][NO][ND]
-@keyword k_AB:  The rate of exchange from site A to B (rad/s).
-@type k_AB: float
-@keyword k_BA:  The rate of exchange from site B to A (rad/s).
-@type k_BA: float
+@keyword kex:   The kex parameter value (the exchange rate in 
rad/s).
+@type kex:  float
 @keyword inv_tcpmg: The inverse of the total duration of the CPMG 
element (in inverse seconds).
 @type inv_tcpmg:numpy float array of rank [NS][NM][NO][ND]
 @keyword tcp:   The tau_CPMG times (1 / 4.nu1).
@@ -133,6 +129,15 @@
 @type power:numpy int array of rank [NS][NM][NO][ND]
 
 
+# Once off parameter conversions.
+pB = 1.0 - pA
+k_BA = pA * kex
+k_AB = pB * kex
+
+# This is a vector that contains the initial magnetizations corresponding 
to the A and B state transverse magnetizations.
+M0[0] = pA
+M0[1] = pB
+
 # Extract shape of experiment.
 NS, NM, NO = num_points.shape
 
@@ -236,7 +241,7 @@
 back_calc[si, mi, oi, i]= -inv_tcpmg[si, mi, oi, i] * 
log(Mx / pA)
 
 
-def r2eff_ns_mmq_2site_sq_dq_zq(M0=None, F_vector=array([1, 0], float64), 
m1=None, m2=None, R20A=None, R20B=None, pA=None, pB=None, dw=None, dwH=None, 
k_AB=None, k_BA=None, inv_tcpmg=None, tcp=None, back_calc=None, 
num_points=None, power=None):
+def r2eff_ns_mmq_2site_sq_dq_zq(M0=None, F_vector=array([1, 0], float64), 
m1=None, m2=None, R20A=None, R20B=None, pA=None, dw=None, dwH=None, kex=None, 
inv_tcpmg=None, tcp=None, back_calc=None, num_points=None, power=None):
 The 2-site numerical solution to the Bloch-McConnell equation for SQ, 
ZQ, and DQ data.
 
 The notation used here comes from:
@@ -260,16 +265,12 @@
 @type R20B: numpy float array of rank [NS][NM][NO][ND]
 @keyword pA:The population of state A.
 @type pA:   float
-@keyword pB:The population of state B.
-@type pB:   float
 @keyword dw:The combined chemical exchange difference between 
states A and B in rad/s.  It should be set to dwH for 1H SQ data, dw for 
heteronuclear SQ data, dwH-dw for ZQ data, and dwH+dw for DQ data.
 @type dw:   numpy float array of rank [NS][NM][NO][ND]
 @keyword dwH:   Unused - this is simply to match the 
r2eff_ns_mmq_2site_mq() function arguments.
 @type dwH:  numpy float array of rank [NS][NM][NO][ND]
-@keyword k_AB:  The rate of exchange from site A to B (rad/s).
-@type k_AB: float
-@keyword k_BA:  The rate of exchange from site B to A (rad/s).
-@type k_BA: float
+@keyword kex:   The kex parameter value (the exchange rate in 
rad/s).
+@type kex

r24115 - in /branches/disp_spin_speed: lib/dispersion/ns_r1rho_2site.py target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 17:57:44 2014
New Revision: 24115

URL: http://svn.gna.org/viewcvs/relax?rev=24115view=rev
Log:
Moved the parameter conversion from target function to lib function for NS 
r1rho 2site.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py?rev=24115r1=24114r2=24115view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   Wed Jun 18 
17:57:44 2014
@@ -59,7 +59,7 @@
 from lib.linear_algebra.matrix_exponential import matrix_exponential
 
 
-def ns_r1rho_2site(M0=None, matrix=None, r1rho_prime=None, omega=None, 
offset=None, r1=0.0, pA=None, pB=None, dw=None, k_AB=None, k_BA=None, 
spin_lock_fields=None, relax_time=None, inv_relax_time=None, back_calc=None, 
num_points=None):
+def ns_r1rho_2site(M0=None, matrix=None, r1rho_prime=None, omega=None, 
offset=None, r1=0.0, pA=None, dw=None, kex=None, spin_lock_fields=None, 
relax_time=None, inv_relax_time=None, back_calc=None, num_points=None):
 The 2-site numerical solution to the Bloch-McConnell equation for R1rho 
data.
 
 This function calculates and stores the R1rho values.
@@ -79,14 +79,10 @@
 @type r1:   numpy float array of rank [NS][NM][NO][ND]
 @keyword pA:The population of state A.
 @type pA:   float
-@keyword pB:The population of state B.
-@type pB:   float
 @keyword dw:The chemical exchange difference between 
states A and B in rad/s.
 @type dw:   numpy float array of rank [NS][NM][NO][ND]
-@keyword k_AB:  The rate of exchange from site A to B (rad/s).
-@type k_AB: float
-@keyword k_BA:  The rate of exchange from site B to A (rad/s).
-@type k_BA: float
+@keyword kex:   The kex parameter value (the exchange rate in 
rad/s).
+@type kex:  float
 @keyword spin_lock_fields:  The R1rho spin-lock field strengths (in 
rad.s^-1).
 @type spin_lock_fields: numpy float array of rank [NS][NM][NO][ND]
 @keyword relax_time:The total relaxation time period for each 
spin-lock field strength (in seconds).
@@ -98,6 +94,11 @@
 @keyword num_points:The number of points on the dispersion curve, 
equal to the length of the tcp and back_calc arguments.
 @type num_points:   numpy int array of rank [NS][NM][NO]
 
+
+# Once off parameter conversions.
+pB = 1.0 - pA
+k_BA = pA * kex
+k_AB = pB * kex
 
 # Extract shape of experiment.
 NE, NS, NM, NO = num_points.shape

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24115r1=24114r2=24115view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Wed Jun 18 
17:57:44 2014
@@ -1621,11 +1621,6 @@
 pA = params[self.end_index[1]]
 kex = params[self.end_index[1]+1]
 
-# Once off parameter conversions.
-pB = 1.0 - pA
-k_BA = pA * kex
-k_AB = pB * kex
-
 # Convert dw from ppm to rad/s. Use the out argument, to pass directly 
to structure.
 multiply( multiply.outer( dw.reshape(1, self.NS), self.nm_no_nd_ones 
), self.frqs, out=self.dw_struct )
 
@@ -1633,7 +1628,7 @@
 self.r20_struct[:] = multiply.outer( r1rho_prime.reshape(self.NE, 
self.NS, self.NM), self.no_nd_ones )
 
 # Back calculate the R2eff values.
-ns_r1rho_2site(M0=self.M0, matrix=self.matrix, 
r1rho_prime=self.r20_struct, omega=self.chemical_shifts, offset=self.offset, 
r1=self.r1, pA=pA, pB=pB, dw=self.dw_struct, k_AB=k_AB, k_BA=k_BA, 
spin_lock_fields=self.spin_lock_omega1, relax_time=self.relax_times, 
inv_relax_time=self.inv_relax_times, back_calc=self.back_calc, 
num_points=self.num_disp_points)
+ns_r1rho_2site(M0=self.M0, matrix=self.matrix, 
r1rho_prime=self.r20_struct, omega=self.chemical_shifts, offset=self.offset, 
r1=self.r1, pA=pA, dw=self.dw_struct, kex=kex, 
spin_lock_fields=self.spin_lock_omega1, relax_time=self.relax_times, 
inv_relax_time=self.inv_relax_times, back_calc=self.back_calc, 
num_points=self.num_disp_points)
 
 # Clean the data for all values, which is left over at the end of 
arrays

r24119 - in /branches/disp_spin_speed: lib/dispersion/ns_mmq_3site.py target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 18:52:37 2014
New Revision: 24119

URL: http://svn.gna.org/viewcvs/relax?rev=24119view=rev
Log:
Moved the parameter conversion for ns mmq 3site into lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py?rev=24119r1=24118r2=24119view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py Wed Jun 18 
18:52:37 2014
@@ -110,7 +110,7 @@
 matrix[2, 2] = -k_CB - k_CA + 1.j*dw_AC - R20C
 
 
-def r2eff_ns_mmq_3site_mq(M0=None, F_vector=array([1, 0, 0], float64), 
m1=None, m2=None, R20A=None, R20B=None, R20C=None, pA=None, pB=None, pC=None, 
dw_AB=None, dw_AC=None, dwH_AB=None, dwH_AC=None, k_AB=None, k_BA=None, 
k_BC=None, k_CB=None, k_AC=None, k_CA=None, inv_tcpmg=None, tcp=None, 
back_calc=None, num_points=None, power=None):
+def r2eff_ns_mmq_3site_mq(M0=None, F_vector=array([1, 0, 0], float64), 
m1=None, m2=None, R20A=None, R20B=None, R20C=None, pA=None, pB=None, 
dw_AB=None, dw_AC=None, dwH_AB=None, dwH_AC=None, kex_AB=None, kex_BC=None, 
kex_AC=None, inv_tcpmg=None, tcp=None, back_calc=None, num_points=None, 
power=None):
 The 3-site numerical solution to the Bloch-McConnell equation for MQ 
data.
 
 The notation used here comes from:
@@ -142,8 +142,6 @@
 @type pA:   float
 @keyword pB:The population of state B.
 @type pB:   float
-@keyword pC:The population of state C.
-@type pC:   float
 @keyword dw_AB: The chemical exchange difference between states A 
and B in rad/s.
 @type dw_AB:numpy float array of rank [NS][NM][NO][ND]
 @keyword dw_AC: The chemical exchange difference between states A 
and C in rad/s.
@@ -152,18 +150,12 @@
 @type dwH_AB:   numpy float array of rank [NS][NM][NO][ND]
 @keyword dwH_AC:The proton chemical exchange difference between 
states A and C in rad/s.
 @type dwH_AC:   numpy float array of rank [NS][NM][NO][ND]
-@keyword k_AB:  The rate of exchange from site A to B (rad/s).
-@type k_AB: float
-@keyword k_BA:  The rate of exchange from site B to A (rad/s).
-@type k_BA: float
-@keyword k_BC:  The rate of exchange from site B to C (rad/s).
-@type k_BC: float
-@keyword k_CB:  The rate of exchange from site C to B (rad/s).
-@type k_CB: float
-@keyword k_AC:  The rate of exchange from site A to C (rad/s).
-@type k_AC: float
-@keyword k_CA:  The rate of exchange from site C to A (rad/s).
-@type k_CA: float
+@keyword kex_AB:The exchange rate between sites A and B for 3-site 
exchange with kex_AB = k_AB + k_BA (rad.s^-1)
+@type kex_AB:   float
+@keyword kex_BC:The exchange rate between sites A and C for 3-site 
exchange with kex_AC = k_AC + k_CA (rad.s^-1)
+@type kex_BC:   float
+@keyword kex_AC:The exchange rate between sites B and C for 3-site 
exchange with kex_BC = k_BC + k_CB (rad.s^-1)
+@type kex_AC:   float
 @keyword inv_tcpmg: The inverse of the total duration of the CPMG 
element (in inverse seconds).
 @type inv_tcpmg:float
 @keyword tcp:   The tau_CPMG times (1 / 4.nu1).
@@ -176,6 +168,23 @@
 @type power:numpy int array of rank [NS][NM][NO][ND]
 
 
+# Once off parameter conversions.
+pC = 1.0 - pA - pB
+pA_pB = pA + pB
+pA_pC = pA + pC
+pB_pC = pB + pC
+k_BA = pA * kex_AB / pA_pB
+k_AB = pB * kex_AB / pA_pB
+k_CB = pB * kex_BC / pB_pC
+k_BC = pC * kex_BC / pB_pC
+k_CA = pA * kex_AC / pA_pC
+k_AC = pC * kex_AC / pA_pC
+
+# This is a vector that contains the initial magnetizations corresponding 
to the A and B state transverse magnetizations.
+M0[0] = pA
+M0[1] = pB
+M0[2] = pC
+
 # Extract shape of experiment.
 NS, NM, NO = num_points.shape
 
@@ -283,7 +292,7 @@
 back_calc[si, mi, oi, i]= -inv_tcpmg[si, mi, oi, i] * 
log(Mx / pA)
 
 
-def r2eff_ns_mmq_3site_sq_dq_zq(M0=None, F_vector=array([1, 0, 0], float64), 
m1=None, m2=None, R20A=None, R20B=None, R20C=None, pA=None, pB=None, pC=None, 
dw_AB=None, dw_AC=None, dwH_AB=None, dwH_AC=None, k_AB=None, k_BA=None, 
k_BC=None, k_CB=None, k_AC=None, k_CA=None, inv_tcpmg=None, tcp=None, 
back_calc=None, num_points=None, power=None):
+def

r24121 - in /branches/disp_spin_speed: lib/dispersion/ns_r1rho_3site.py target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:01:24 2014
New Revision: 24121

URL: http://svn.gna.org/viewcvs/relax?rev=24121view=rev
Log:
Moved the parameter conversion for r1rho 3site into lib function.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py
branches/disp_spin_speed/target_functions/relax_disp.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py?rev=24121r1=24120r2=24121view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py   (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py   Wed Jun 18 
19:01:24 2014
@@ -65,7 +65,7 @@
 from lib.linear_algebra.matrix_exponential import matrix_exponential
 
 
-def ns_r1rho_3site(M0=None, matrix=None, r1rho_prime=None, omega=None, 
offset=None, r1=0.0, pA=None, pB=None, pC=None, dw_AB=None, dw_AC=None, 
k_AB=None, k_BA=None, k_BC=None, k_CB=None, k_AC=None, k_CA=None, 
spin_lock_fields=None, relax_time=None, inv_relax_time=None, back_calc=None, 
num_points=None):
+def ns_r1rho_3site(M0=None, matrix=None, r1rho_prime=None, omega=None, 
offset=None, r1=0.0, pA=None, pB=None, dw_AB=None, dw_AC=None, kex_AB=None, 
kex_BC=None, kex_AC=None, spin_lock_fields=None, relax_time=None, 
inv_relax_time=None, back_calc=None, num_points=None):
 The 3-site numerical solution to the Bloch-McConnell equation for R1rho 
data.
 
 This function calculates and stores the R1rho values.
@@ -87,24 +87,16 @@
 @type pA:   float
 @keyword pB:The population of state B.
 @type pB:   float
-@keyword pC:The population of state C.
-@type pC:   float
 @keyword dw_AB: The chemical exchange difference between 
states A and B in rad/s.
 @type dw_AB:numpy float array of rank [NS][NM][NO][ND]
 @keyword dw_AC: The chemical exchange difference between 
states A and C in rad/s.
 @type dw_AC:numpy float array of rank [NS][NM][NO][ND]
-@keyword k_AB:  The rate of exchange from site A to B (rad/s).
-@type k_AB: float
-@keyword k_BA:  The rate of exchange from site B to A (rad/s).
-@type k_BA: float
-@keyword k_BC:  The rate of exchange from site B to C (rad/s).
-@type k_BC: float
-@keyword k_CB:  The rate of exchange from site C to B (rad/s).
-@type k_CB: float
-@keyword k_AC:  The rate of exchange from site A to C (rad/s).
-@type k_AC: float
-@keyword k_CA:  The rate of exchange from site C to A (rad/s).
-@type k_CA: float
+@keyword kex_AB:The exchange rate between sites A and B for 
3-site exchange with kex_AB = k_AB + k_BA (rad.s^-1)
+@type kex_AB:   float
+@keyword kex_BC:The exchange rate between sites A and C for 
3-site exchange with kex_AC = k_AC + k_CA (rad.s^-1)
+@type kex_BC:   float
+@keyword kex_AC:The exchange rate between sites B and C for 
3-site exchange with kex_BC = k_BC + k_CB (rad.s^-1)
+@type kex_AC:   float
 @keyword spin_lock_fields:  The R1rho spin-lock field strengths (in 
rad.s^-1).
 @type spin_lock_fields: numpy float array of rank [NS][NM][NO][ND]
 @keyword relax_time:The total relaxation time period for each 
spin-lock field strength (in seconds).
@@ -116,6 +108,18 @@
 @keyword num_points:The number of points on the dispersion curve, 
equal to the length of the tcp and back_calc arguments.
 @type num_points:   numpy int array of rank [NS][NM][NO]
 
+
+# Once off parameter conversions.
+pC = 1.0 - pA - pB
+pA_pB = pA + pB
+pA_pC = pA + pC
+pB_pC = pB + pC
+k_BA = pA * kex_AB / pA_pB
+k_AB = pB * kex_AB / pA_pB
+k_CB = pB * kex_BC / pB_pC
+k_BC = pC * kex_BC / pB_pC
+k_CA = pA * kex_AC / pA_pC
+k_AC = pC * kex_AC / pA_pC
 
 # Extract shape of experiment.
 NE, NS, NM, NO = num_points.shape

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24121r1=24120r2=24121view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Wed Jun 18 
19:01:24 2014
@@ -765,16 +765,6 @@
 
 
 # Once off parameter conversions.
-pC = 1.0 - pA - pB
-pA_pB

r24122 - in /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling: profiling_cr72.py profiling_cr72_full.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:03:08 2014
New Revision: 24122

URL: http://svn.gna.org/viewcvs/relax?rev=24122view=rev
Log:
Copied profiling script for CR72, so there is now a normal and a full version.


Added:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py
  - copied unchanged from r24121, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72_full.py
  - copied unchanged from r24121, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py


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r24123 - in /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling: profiling_b14.py profiling_b14_full.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:04:01 2014
New Revision: 24123

URL: http://svn.gna.org/viewcvs/relax?rev=24123view=rev
Log:
Copied profiling for b14 to normal and full model.


Added:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py
  - copied unchanged from r24121, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14_full.py
  - copied unchanged from r24121, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py


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r24125 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:10:13 2014
New Revision: 24125

URL: http://svn.gna.org/viewcvs/relax?rev=24125view=rev
Log:
Copied profiling script for cpmg 3D.

Added:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
  - copied unchanged from r24121, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D_full.py
  - copied unchanged from r24121, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py


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r24126 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:11:10 2014
New Revision: 24126

URL: http://svn.gna.org/viewcvs/relax?rev=24126view=rev
Log:
Copied profiling script for ns cpmg star.

Added:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star.py
  - copied unchanged from r24125, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star_full.py
  - copied unchanged from r24125, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D_full.py


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r24127 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_norex.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:12:12 2014
New Revision: 24127

URL: http://svn.gna.org/viewcvs/relax?rev=24127view=rev
Log:
copied profiling script for no rex.

Added:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_norex.py
  - copied unchanged from r24122, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py


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r24128 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:15:19 2014
New Revision: 24128

URL: http://svn.gna.org/viewcvs/relax?rev=24128view=rev
Log:
Modified profiling script for B14, to R20A=R20B.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py?rev=24128r1=24127r2=24128view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py
   (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py
   Wed Jun 18 19:15:19 2014
@@ -436,7 +436,7 @@
 return chi2
 
 
-def single(num_spins=1, model=MODEL_B14_FULL, iter=None):
+def single(num_spins=1, model=MODEL_B14, iter=None):
 Calculate for a single spin.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -450,7 +450,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Loop 100 times for each spin in the clustered analysis (to make the 
timing numbers equivalent).
 for spin_index in xrange(100):
@@ -460,7 +460,7 @@
 print(chi2 single:, chi2)
 
 
-def cluster(num_spins=100, model=MODEL_B14_FULL, iter=None):
+def cluster(num_spins=100, model=MODEL_B14, iter=None):
 Calculate for a number of clustered spins.
 
 @keyword num_spins: Number of spins in the cluster.


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r24129 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:20:19 2014
New Revision: 24129

URL: http://svn.gna.org/viewcvs/relax?rev=24129view=rev
Log:
Removal of junk, and replacing func.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py?rev=24129r1=24128r2=24129view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py
   (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14.py
   Wed Jun 18 19:20:19 2014
@@ -55,7 +55,7 @@
 from lib.physical_constants import g1H, g15N
 from target_functions.chi2 import chi2
 from target_functions.relax_disp import Dispersion
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ, 
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_NS_CPMG_2SITE_3D_FULL, 
MODEL_NS_CPMG_2SITE_STAR_FULL
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ, 
MODEL_B14, MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL
 
 
 # Alter setup.
@@ -188,27 +188,6 @@
 @return:The numpy array structures of the R2eff/R1rho values, 
errors, missing data, and corresponding Larmor frequencies.  For each 
structure, the first dimension corresponds to the experiment types, the second 
the spins of a spin block, the third to the spectrometer field strength, and 
the fourth is the dispersion points.  For the Larmor frequency structure, the 
fourth dimension is omitted.  For R1rho-type data, an offset dimension is 
inserted between the spectrometer field strength and the dispersion points.
 @rtype: lists of numpy float arrays, lists of numpy float 
arrays, lists of numpy float arrays, numpy rank-2 int array
 
-
-# Unpack the parameter values.
-# Initialise the post spin parameter indices.
-end_index = []
-# The spin and frequency dependent R2 parameters.
-end_index.append(len(self.exp_type) * self.num_spins * 
len(self.fields))
-if self.model in [MODEL_B14_FULL, MODEL_CR72_FULL, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
-end_index.append(2 * len(self.exp_type) * self.num_spins * 
len(self.fields))
-# The spin and dependent parameters (phi_ex, dw, padw2).
-end_index.append(end_index[-1] + self.num_spins)
-
-# Unpack the parameter values.
-R20 = self.params[:end_index[1]].reshape(self.num_spins*2, 
len(self.fields))
-R20A = R20[::2].flatten()
-R20B = R20[1::2].flatten()
-dw = self.params[end_index[1]:end_index[2]]
-pA = self.params[end_index[2]]
-kex = self.params[end_index[2]+1]
-pB = 1.0 - pA
-k_BA = pA * kex
-k_AB = pB * kex
 
 # Initialise the data structures for the target function.
 exp_types = []
@@ -280,13 +259,6 @@
 # Get the cpmg frq.
 cpmg_frqs[ei][mi][oi] = self.points[mi]
 
-# Calculate how the value should be, so chi2 gets zero.
-# The R20 index.
-r20_index = mi + si*len(self.fields)
-# Convert dw from ppm to rad/s.
-dw_frq = dw[si] * frqs[ei][si][mi]
-r20a=R20A[r20_index]
-r20b=R20B[r20_index]
 back_calc = array([0.0]*len(cpmg_frqs[ei][mi][oi]))
 
 for oi in range(len(self.offset)):
@@ -432,7 +404,7 @@
 
 
 # Return chi2 value.
-chi2 = self.model.func_B14_full(params)
+chi2 = self.model.func_B14(params)
 return chi2
 
 
@@ -474,7 +446,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Repeat the function call, to simulate minimisation.
 for i in xrange(iter):
@@ -485,38 +457,3 @@
 # Execute main function.
 if __name__ == __main__:
 main()
-
-def test_reshape():
-C1 = Profile(num_spins=1, model=MODEL_B14_FULL, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
-end_index = C1.model.end_index
-#print(end_index:, end_index)
-num_spins = C1.model.num_spins
-#print(num_spins:, num_spins)
-num_frq = C1.model.num_frq
-#print(num_frq:, num_frq)
-params = C1.params

r24130 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14_full.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:20:21 2014
New Revision: 24130

URL: http://svn.gna.org/viewcvs/relax?rev=24130view=rev
Log:
Removal of junk from profiling script.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14_full.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14_full.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14_full.py?rev=24130r1=24129r2=24130view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14_full.py
  (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_b14_full.py
  Wed Jun 18 19:20:21 2014
@@ -188,27 +188,6 @@
 @return:The numpy array structures of the R2eff/R1rho values, 
errors, missing data, and corresponding Larmor frequencies.  For each 
structure, the first dimension corresponds to the experiment types, the second 
the spins of a spin block, the third to the spectrometer field strength, and 
the fourth is the dispersion points.  For the Larmor frequency structure, the 
fourth dimension is omitted.  For R1rho-type data, an offset dimension is 
inserted between the spectrometer field strength and the dispersion points.
 @rtype: lists of numpy float arrays, lists of numpy float 
arrays, lists of numpy float arrays, numpy rank-2 int array
 
-
-# Unpack the parameter values.
-# Initialise the post spin parameter indices.
-end_index = []
-# The spin and frequency dependent R2 parameters.
-end_index.append(len(self.exp_type) * self.num_spins * 
len(self.fields))
-if self.model in [MODEL_B14_FULL, MODEL_CR72_FULL, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
-end_index.append(2 * len(self.exp_type) * self.num_spins * 
len(self.fields))
-# The spin and dependent parameters (phi_ex, dw, padw2).
-end_index.append(end_index[-1] + self.num_spins)
-
-# Unpack the parameter values.
-R20 = self.params[:end_index[1]].reshape(self.num_spins*2, 
len(self.fields))
-R20A = R20[::2].flatten()
-R20B = R20[1::2].flatten()
-dw = self.params[end_index[1]:end_index[2]]
-pA = self.params[end_index[2]]
-kex = self.params[end_index[2]+1]
-pB = 1.0 - pA
-k_BA = pA * kex
-k_AB = pB * kex
 
 # Initialise the data structures for the target function.
 exp_types = []
@@ -280,13 +259,6 @@
 # Get the cpmg frq.
 cpmg_frqs[ei][mi][oi] = self.points[mi]
 
-# Calculate how the value should be, so chi2 gets zero.
-# The R20 index.
-r20_index = mi + si*len(self.fields)
-# Convert dw from ppm to rad/s.
-dw_frq = dw[si] * frqs[ei][si][mi]
-r20a=R20A[r20_index]
-r20b=R20B[r20_index]
 back_calc = array([0.0]*len(cpmg_frqs[ei][mi][oi]))
 
 for oi in range(len(self.offset)):
@@ -484,39 +456,4 @@
 
 # Execute main function.
 if __name__ == __main__:
-main()
-
-def test_reshape():
-C1 = Profile(num_spins=1, model=MODEL_B14_FULL, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
-end_index = C1.model.end_index
-#print(end_index:, end_index)
-num_spins = C1.model.num_spins
-#print(num_spins:, num_spins)
-num_frq = C1.model.num_frq
-#print(num_frq:, num_frq)
-params = C1.params
-#print(params, params)
-
-R20 = params[:end_index[1]].reshape(num_spins*2, num_frq)
-R20A = R20[::2].flatten()
-R20B = R20[1::2].flatten()
-dw = params[end_index[1]:end_index[2]]
-pA = params[end_index[2]]
-kex = params[end_index[2]+1]
-print(R20A, R20A, len(R20A))
-print(R20B, R20B, len(R20B))
-print(dw, dw, len(dw))
-print(dw, pA)
-print(kex, kex)
-
-for si in range(num_spins):
-for mi in range(num_frq):
-r20_index = mi + si*num_frq
-r20a=R20A[r20_index]
-r20b=R20B[r20_index]
-print(r20a, r20a, r20b, r20b)
-
-model = C1.calc(params)
-print(model)
-
-#test_reshape()
+main()


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r24132 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:25:31 2014
New Revision: 24132

URL: http://svn.gna.org/viewcvs/relax?rev=24132view=rev
Log:
Removal of junk from profiling script CR72 and making it work.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py?rev=24132r1=24131r2=24132view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py
  (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py
  Wed Jun 18 19:25:31 2014
@@ -183,24 +183,6 @@
 @return:The numpy array structures of the R2eff/R1rho values, 
errors, missing data, and corresponding Larmor frequencies.  For each 
structure, the first dimension corresponds to the experiment types, the second 
the spins of a spin block, the third to the spectrometer field strength, and 
the fourth is the dispersion points.  For the Larmor frequency structure, the 
fourth dimension is omitted.  For R1rho-type data, an offset dimension is 
inserted between the spectrometer field strength and the dispersion points.
 @rtype: lists of numpy float arrays, lists of numpy float 
arrays, lists of numpy float arrays, numpy rank-2 int array
 
-
-# Unpack the parameter values.
-# Initialise the post spin parameter indices.
-end_index = []
-# The spin and frequency dependent R2 parameters.
-end_index.append(len(self.exp_type) * self.num_spins * 
len(self.fields))
-if self.model in [MODEL_B14_FULL, MODEL_CR72_FULL, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
-end_index.append(2 * len(self.exp_type) * self.num_spins * 
len(self.fields))
-# The spin and dependent parameters (phi_ex, dw, padw2).
-end_index.append(end_index[-1] + self.num_spins)
-
-# Unpack the parameter values.
-R20 = self.params[:end_index[1]].reshape(self.num_spins*2, 
len(self.fields))
-R20A = R20[::2].flatten()
-R20B = R20[1::2].flatten()
-dw = self.params[end_index[1]:end_index[2]]
-pA = self.params[end_index[2]]
-kex = self.params[end_index[2]+1]
 
 # Initialise the data structures for the target function.
 exp_types = []
@@ -272,13 +254,6 @@
 # Get the cpmg frq.
 cpmg_frqs[ei][mi][oi] = self.points[mi]
 
-# Calculate how the value should be, so chi2 gets zero.
-# The R20 index.
-r20_index = mi + si*len(self.fields)
-# Convert dw from ppm to rad/s.
-dw_frq = dw[si] * frqs[ei][si][mi]
-r20a=R20A[r20_index]
-r20b=R20B[r20_index]
 back_calc = array([0.0]*len(cpmg_frqs[ei][mi][oi]))
 
 for oi in range(len(self.offset)):
@@ -424,11 +399,11 @@
 
 
 # Return chi2 value.
-chi2 = self.model.func_CR72_full(params)
+chi2 = self.model.func_CR72(params)
 return chi2
 
 
-def single(num_spins=1, model=MODEL_CR72_FULL, iter=None):
+def single(num_spins=1, model=MODEL_CR72, iter=None):
 Calculate for a single spin.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -442,7 +417,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Loop 100 times for each spin in the clustered analysis (to make the 
timing numbers equivalent).
 for spin_index in xrange(100):
@@ -452,7 +427,7 @@
 print(chi2 single:, chi2)
 
 
-def cluster(num_spins=100, model=MODEL_CR72_FULL, iter=None):
+def cluster(num_spins=100, model=MODEL_CR72, iter=None):
 Calculate for a number of clustered spins.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -466,7 +441,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Repeat the function call, to simulate minimisation.
 for i in xrange(iter):
@@ -476,39 +451,4 @@
 
 # Execute main function.
 if __name__ == __main__:
-main()
-
-def

r24131 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72_full.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:25:29 2014
New Revision: 24131

URL: http://svn.gna.org/viewcvs/relax?rev=24131view=rev
Log:
Removal of junk for profiling script CR72 full.
Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72_full.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72_full.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72_full.py?rev=24131r1=24130r2=24131view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72_full.py
 (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72_full.py
 Wed Jun 18 19:25:29 2014
@@ -183,24 +183,6 @@
 @return:The numpy array structures of the R2eff/R1rho values, 
errors, missing data, and corresponding Larmor frequencies.  For each 
structure, the first dimension corresponds to the experiment types, the second 
the spins of a spin block, the third to the spectrometer field strength, and 
the fourth is the dispersion points.  For the Larmor frequency structure, the 
fourth dimension is omitted.  For R1rho-type data, an offset dimension is 
inserted between the spectrometer field strength and the dispersion points.
 @rtype: lists of numpy float arrays, lists of numpy float 
arrays, lists of numpy float arrays, numpy rank-2 int array
 
-
-# Unpack the parameter values.
-# Initialise the post spin parameter indices.
-end_index = []
-# The spin and frequency dependent R2 parameters.
-end_index.append(len(self.exp_type) * self.num_spins * 
len(self.fields))
-if self.model in [MODEL_B14_FULL, MODEL_CR72_FULL, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
-end_index.append(2 * len(self.exp_type) * self.num_spins * 
len(self.fields))
-# The spin and dependent parameters (phi_ex, dw, padw2).
-end_index.append(end_index[-1] + self.num_spins)
-
-# Unpack the parameter values.
-R20 = self.params[:end_index[1]].reshape(self.num_spins*2, 
len(self.fields))
-R20A = R20[::2].flatten()
-R20B = R20[1::2].flatten()
-dw = self.params[end_index[1]:end_index[2]]
-pA = self.params[end_index[2]]
-kex = self.params[end_index[2]+1]
 
 # Initialise the data structures for the target function.
 exp_types = []
@@ -272,13 +254,6 @@
 # Get the cpmg frq.
 cpmg_frqs[ei][mi][oi] = self.points[mi]
 
-# Calculate how the value should be, so chi2 gets zero.
-# The R20 index.
-r20_index = mi + si*len(self.fields)
-# Convert dw from ppm to rad/s.
-dw_frq = dw[si] * frqs[ei][si][mi]
-r20a=R20A[r20_index]
-r20b=R20B[r20_index]
 back_calc = array([0.0]*len(cpmg_frqs[ei][mi][oi]))
 
 for oi in range(len(self.offset)):
@@ -476,39 +451,4 @@
 
 # Execute main function.
 if __name__ == __main__:
-main()
-
-def test_reshape():
-C1 = Profile(num_spins=1, model=MODEL_CR72_FULL, r2a=5.0, r2b=10.0, 
dw=3.0, pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
-end_index = C1.model.end_index
-#print(end_index:, end_index)
-num_spins = C1.model.num_spins
-#print(num_spins:, num_spins)
-num_frq = C1.model.num_frq
-#print(num_frq:, num_frq)
-params = C1.params
-#print(params, params)
-
-R20 = params[:end_index[1]].reshape(num_spins*2, num_frq)
-R20A = R20[::2].flatten()
-R20B = R20[1::2].flatten()
-dw = params[end_index[1]:end_index[2]]
-pA = params[end_index[2]]
-kex = params[end_index[2]+1]
-print(R20A, R20A, len(R20A))
-print(R20B, R20B, len(R20B))
-print(dw, dw, len(dw))
-print(dw, pA)
-print(kex, kex)
-
-for si in range(num_spins):
-for mi in range(num_frq):
-r20_index = mi + si*num_frq
-r20a=R20A[r20_index]
-r20b=R20B[r20_index]
-print(r20a, r20a, r20b, r20b)
-
-model = C1.calc(params)
-print(model)
-
-#test_reshape()
+main()


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r24133 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_norex.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:29:28 2014
New Revision: 24133

URL: http://svn.gna.org/viewcvs/relax?rev=24133view=rev
Log:
Removal of junk, and implementing NO REX profiling script.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_norex.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_norex.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_norex.py?rev=24133r1=24132r2=24133view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_norex.py
 (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_norex.py
 Wed Jun 18 19:29:28 2014
@@ -55,7 +55,7 @@
 from lib.physical_constants import g1H, g15N
 from target_functions.chi2 import chi2
 from target_functions.relax_disp import Dispersion
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ, 
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_NS_CPMG_2SITE_3D_FULL, 
MODEL_NS_CPMG_2SITE_STAR_FULL
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ, 
MODEL_NOREX, MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL
 
 
 # Alter setup.
@@ -183,24 +183,6 @@
 @return:The numpy array structures of the R2eff/R1rho values, 
errors, missing data, and corresponding Larmor frequencies.  For each 
structure, the first dimension corresponds to the experiment types, the second 
the spins of a spin block, the third to the spectrometer field strength, and 
the fourth is the dispersion points.  For the Larmor frequency structure, the 
fourth dimension is omitted.  For R1rho-type data, an offset dimension is 
inserted between the spectrometer field strength and the dispersion points.
 @rtype: lists of numpy float arrays, lists of numpy float 
arrays, lists of numpy float arrays, numpy rank-2 int array
 
-
-# Unpack the parameter values.
-# Initialise the post spin parameter indices.
-end_index = []
-# The spin and frequency dependent R2 parameters.
-end_index.append(len(self.exp_type) * self.num_spins * 
len(self.fields))
-if self.model in [MODEL_B14_FULL, MODEL_CR72_FULL, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL]:
-end_index.append(2 * len(self.exp_type) * self.num_spins * 
len(self.fields))
-# The spin and dependent parameters (phi_ex, dw, padw2).
-end_index.append(end_index[-1] + self.num_spins)
-
-# Unpack the parameter values.
-R20 = self.params[:end_index[1]].reshape(self.num_spins*2, 
len(self.fields))
-R20A = R20[::2].flatten()
-R20B = R20[1::2].flatten()
-dw = self.params[end_index[1]:end_index[2]]
-pA = self.params[end_index[2]]
-kex = self.params[end_index[2]+1]
 
 # Initialise the data structures for the target function.
 exp_types = []
@@ -272,13 +254,6 @@
 # Get the cpmg frq.
 cpmg_frqs[ei][mi][oi] = self.points[mi]
 
-# Calculate how the value should be, so chi2 gets zero.
-# The R20 index.
-r20_index = mi + si*len(self.fields)
-# Convert dw from ppm to rad/s.
-dw_frq = dw[si] * frqs[ei][si][mi]
-r20a=R20A[r20_index]
-r20b=R20B[r20_index]
 back_calc = array([0.0]*len(cpmg_frqs[ei][mi][oi]))
 
 for oi in range(len(self.offset)):
@@ -424,11 +399,11 @@
 
 
 # Return chi2 value.
-chi2 = self.model.func_CR72_full(params)
+chi2 = self.model.func_NOREX(params)
 return chi2
 
 
-def single(num_spins=1, model=MODEL_CR72_FULL, iter=None):
+def single(num_spins=1, model=MODEL_NOREX, iter=None):
 Calculate for a single spin.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -442,7 +417,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, spins_params=['r2'])
 
 # Loop 100 times for each spin in the clustered analysis (to make the 
timing numbers equivalent).
 for spin_index in xrange(100):
@@ -452,7 +427,7 @@
 print(chi2 single:, chi2)
 
 
-def cluster(num_spins=100, model=MODEL_CR72_FULL, iter=None):
+def cluster(num_spins=100, model=MODEL_NOREX, iter=None):
 Calculate for a number of clustered spins.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -466,7 +441,7

r24134 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:32:18 2014
New Revision: 24134

URL: http://svn.gna.org/viewcvs/relax?rev=24134view=rev
Log:
Implemented profiling script for NS CPMG 2site 3D.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py?rev=24134r1=24133r2=24134view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
  (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_3D.py
  Wed Jun 18 19:32:18 2014
@@ -400,11 +400,11 @@
 
 
 # Return chi2 value.
-chi2 = self.model.func_ns_cpmg_2site_3D_full(params)
+chi2 = self.model.func_ns_cpmg_2site_3D(params)
 return chi2
 
 
-def single(num_spins=1, model=MODEL_NS_CPMG_2SITE_3D_FULL, iter=None):
+def single(num_spins=1, model=MODEL_NS_CPMG_2SITE_3D, iter=None):
 Calculate for a single spin.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -418,7 +418,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Loop 100 times for each spin in the clustered analysis (to make the 
timing numbers equivalent).
 for spin_index in xrange(100):
@@ -428,7 +428,7 @@
 print(chi2 single:, chi2)
 
 
-def cluster(num_spins=100, model=MODEL_NS_CPMG_2SITE_3D_FULL, iter=None):
+def cluster(num_spins=100, model=MODEL_NS_CPMG_2SITE_3D, iter=None):
 Calculate for a number of clustered spins.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -442,7 +442,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Repeat the function call, to simulate minimisation.
 for i in xrange(iter):


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r24135 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:36:48 2014
New Revision: 24135

URL: http://svn.gna.org/viewcvs/relax?rev=24135view=rev
Log:
Implemented profiling script for NS CPMG STAR and STAR FULL.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star.py

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star_full.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star.py?rev=24135r1=24134r2=24135view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star.py
(original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star.py
Wed Jun 18 19:36:48 2014
@@ -55,7 +55,7 @@
 from lib.physical_constants import g1H, g15N
 from target_functions.chi2 import chi2
 from target_functions.relax_disp import Dispersion
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ, 
MODEL_B14_FULL, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, 
MODEL_NS_CPMG_2SITE_STAR_FULL
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ, 
MODEL_B14_FULL, MODEL_NS_CPMG_2SITE_3D, MODEL_NS_CPMG_2SITE_3D_FULL, 
MODEL_NS_CPMG_2SITE_STAR, MODEL_NS_CPMG_2SITE_STAR_FULL
 
 
 # Alter setup.
@@ -400,11 +400,11 @@
 
 
 # Return chi2 value.
-chi2 = self.model.func_ns_cpmg_2site_3D_full(params)
+chi2 = self.model.func_ns_cpmg_2site_star(params)
 return chi2
 
 
-def single(num_spins=1, model=MODEL_NS_CPMG_2SITE_3D_FULL, iter=None):
+def single(num_spins=1, model=MODEL_NS_CPMG_2SITE_STAR, iter=None):
 Calculate for a single spin.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -418,7 +418,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Loop 100 times for each spin in the clustered analysis (to make the 
timing numbers equivalent).
 for spin_index in xrange(100):
@@ -428,7 +428,7 @@
 print(chi2 single:, chi2)
 
 
-def cluster(num_spins=100, model=MODEL_NS_CPMG_2SITE_3D_FULL, iter=None):
+def cluster(num_spins=100, model=MODEL_NS_CPMG_2SITE_STAR, iter=None):
 Calculate for a number of clustered spins.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -442,7 +442,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2a=5.0, r2b=10.0, dw=3.0, 
pA=0.9, kex=1000.0, spins_params=['r2a', 'r2b', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
 
 # Repeat the function call, to simulate minimisation.
 for i in xrange(iter):

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star_full.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star_full.py?rev=24135r1=24134r2=24135view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star_full.py
   (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_ns_cpmg_2site_star_full.py
   Wed Jun 18 19:36:48 2014
@@ -400,11 +400,11 @@
 
 
 # Return chi2 value.
-chi2 = self.model.func_ns_cpmg_2site_3D_full(params)
+chi2 = self.model.func_ns_cpmg_2site_star_full(params)
 return chi2
 
 
-def single(num_spins=1, model=MODEL_NS_CPMG_2SITE_3D_FULL, iter=None):
+def single(num_spins=1, model=MODEL_NS_CPMG_2SITE_STAR_FULL, iter=None):
 Calculate for a single spin.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -428,7 +428,7 @@
 print(chi2 single:, chi2)
 
 
-def cluster(num_spins=100, model=MODEL_NS_CPMG_2SITE_3D_FULL, iter=None):
+def cluster(num_spins=100, model=MODEL_NS_CPMG_2SITE_STAR_FULL, iter=None):
 Calculate for a number of clustered spins.
 
 @keyword num_spins: Number of spins in the cluster.


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r24136 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:39:44 2014
New Revision: 24136

URL: http://svn.gna.org/viewcvs/relax?rev=24136view=rev
Log:
Copied profiling script to be used for LM63.

Added:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63.py
  - copied unchanged from r24135, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py


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r24137 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_it99.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 19:41:27 2014
New Revision: 24137

URL: http://svn.gna.org/viewcvs/relax?rev=24137view=rev
Log:
Copied profiling script to model IT99.


Added:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_it99.py
  - copied unchanged from r24135, 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_cr72.py


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r24138 - /trunk/target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 20:02:00 2014
New Revision: 24138

URL: http://svn.gna.org/viewcvs/relax?rev=24138view=rev
Log:
Fixed the packing out of paramter tex for global analysis in model IT99.

bug #0(https://gna.org/bugs/index.php?0): Unpacking of parameters for 
global analysis in model IT99, is performed wrong.

Modified:
trunk/target_functions/relax_disp.py

Modified: trunk/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/target_functions/relax_disp.py?rev=24138r1=24137r2=24138view=diff
==
--- trunk/target_functions/relax_disp.py(original)
+++ trunk/target_functions/relax_disp.pyWed Jun 18 20:02:00 2014
@@ -998,7 +998,7 @@
 R20 = params[:self.end_index[0]]
 dw = params[self.end_index[0]:self.end_index[1]]
 pA = params[self.end_index[1]]
-tex = params[self.end_index[2]]
+tex = params[self.end_index[1]+1]
 
 # Once off parameter conversions.
 pB = 1.0 - pA


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r24139 - in /branches/disp_spin_speed: ./ target_functions/relax_disp.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 20:03:09 2014
New Revision: 24139

URL: http://svn.gna.org/viewcvs/relax?rev=24139view=rev
Log:
Merged revisions 24138 via svnmerge from 
svn+ssh://tlin...@svn.gna.org/svn/relax/trunk


  r24138 | tlinnet | 2014-06-18 20:02:00 +0200 (Wed, 18 Jun 2014) | 3 lines
  
  Fixed the packing out of paramter tex for global analysis in model IT99.
  
  bug #0(https://gna.org/bugs/index.php?0): Unpacking of parameters for 
global analysis in model IT99, is performed wrong.


Modified:
branches/disp_spin_speed/   (props changed)
branches/disp_spin_speed/target_functions/relax_disp.py

Propchange: branches/disp_spin_speed/
--
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Jun 18 20:03:09 2014
@@ -1 +1 @@
-/trunk:1-24082
+/trunk:1-24138

Modified: branches/disp_spin_speed/target_functions/relax_disp.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/target_functions/relax_disp.py?rev=24139r1=24138r2=24139view=diff
==
--- branches/disp_spin_speed/target_functions/relax_disp.py (original)
+++ branches/disp_spin_speed/target_functions/relax_disp.py Wed Jun 18 
20:03:09 2014
@@ -994,7 +994,7 @@
 R20 = params[:self.end_index[0]]
 dw = params[self.end_index[0]:self.end_index[1]]
 pA = params[self.end_index[1]]
-tex = params[self.end_index[2]]
+tex = params[self.end_index[1]+1]
 
 # Convert dw from ppm to rad/s. Use the out argument, to pass directly 
to structure.
 multiply( multiply.outer( dw.reshape(1, self.NS), self.nm_no_nd_ones 
), self.frqs, out=self.dw_struct )


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r24141 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 20:17:29 2014
New Revision: 24141

URL: http://svn.gna.org/viewcvs/relax?rev=24141view=rev
Log:
Implemented profiling script for LM63.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63.py?rev=24141r1=24140r2=24141view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63.py
  (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_lm63.py
  Wed Jun 18 20:17:29 2014
@@ -55,7 +55,7 @@
 from lib.physical_constants import g1H, g15N
 from target_functions.chi2 import chi2
 from target_functions.relax_disp import Dispersion
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ, 
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_NS_CPMG_2SITE_3D_FULL, 
MODEL_NS_CPMG_2SITE_STAR_FULL
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ, 
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_LM63, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL
 
 
 # Alter setup.
@@ -110,7 +110,7 @@
 Class Profile inherits the Dispersion container class object.
 
 
-def __init__(self, num_spins=1, model=None, r2=None, r2a=None, r2b=None, 
dw=None, pA=None, kex=None, spins_params=None):
+def __init__(self, num_spins=1, model=None, r2=None, r2a=None, r2b=None, 
phi_ex=None, dw=None, pA=None, kex=None, spins_params=None):
 
 Special method __init__() is called first (acts as Constructor).
 It brings in data from outside the class like the variable num_spins.
@@ -130,6 +130,8 @@
 @type r2a:  float
 @keyword r2b:   The transversal relaxation rate for state B in 
the absence of exchange.
 @type r2b:  float
+@keyword phi_ex:The phi_ex = pA.pB.dw**2 value (ppm^2)
+@type phi_ex:   float
 @keyword dw:The chemical exchange difference between 
states A and B in ppm.
 @type dw:   float
 @keyword pA:The population of state A.
@@ -168,7 +170,7 @@
 self.error.append([1.0]*len(cpmg_point))
 
 # Assemble param vector.
-self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b, 
dw=dw, pA=pA, kex=kex, spins_params=spins_params)
+self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b, 
phi_ex=phi_ex, dw=dw, pA=pA, kex=kex, spins_params=spins_params)
 
 # Make nested list arrays of data. And return them.
 values, errors, cpmg_frqs, missing, frqs, exp_types, relax_times, 
offsets = self.return_r2eff_arrays()
@@ -292,7 +294,7 @@
 return values, errors, cpmg_frqs, missing, frqs, exp_types, 
relax_times, offsets
 
 
-def assemble_param_vector(self, r2=None, r2a=None, r2b=None, dw=None, 
pA=None, kex=None, spins_params=None):
+def assemble_param_vector(self, r2=None, r2a=None, r2b=None, phi_ex=None, 
dw=None, pA=None, kex=None, spins_params=None):
 Assemble the dispersion relaxation dispersion curve fitting 
parameter vector.
 
 @keyword r2:The transversal relaxation rate.
@@ -301,6 +303,8 @@
 @type r2a:  float
 @keyword r2b:   The transversal relaxation rate for state B in 
the absence of exchange.
 @type r2b:  float
+@keyword phi_ex:The phi_ex = pA.pB.dw**2 value (ppm^2)
+@type phi_ex:   float
 @keyword dw:The chemical exchange difference between 
states A and B in ppm.
 @type dw:   float
 @keyword pA:The population of state A.
@@ -327,6 +331,8 @@
 elif param_name == 'r2b':
 value = r2b
 value = value + mi + spin_index*0.1
+elif param_name == 'phi_ex':
+value = phi_ex + spin_index
 elif param_name == 'dw':
 value = dw + spin_index
 elif param_name == 'pA':
@@ -377,6 +383,15 @@
 # Then the chemical shift difference parameters 'phi_ex', 'phi_ex_B', 
'phi_ex_C', 'padw2', 'dw', 'dw_AB', 'dw_BC', 'dw_AB' (one per spin).
 for spin_index in range(self.num_spins):
 
+# Yield the data.
+if 'phi_ex' in spins_params:
+yield 'phi_ex', spin_index, 0
+if 'phi_ex_B' in spins_params:
+yield 'phi_ex_B', spin_index, 0
+if 'phi_ex_C' in spins_params:
+yield 'phi_ex_C', spin_index, 0

r24140 - /branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_it99.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 20:17:26 2014
New Revision: 24140

URL: http://svn.gna.org/viewcvs/relax?rev=24140view=rev
Log:
Added profiling script for IT99.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_it99.py

Modified: 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_it99.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_it99.py?rev=24140r1=24139r2=24140view=diff
==
--- 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_it99.py
  (original)
+++ 
branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/profiling_it99.py
  Wed Jun 18 20:17:26 2014
@@ -55,7 +55,7 @@
 from lib.physical_constants import g1H, g15N
 from target_functions.chi2 import chi2
 from target_functions.relax_disp import Dispersion
-from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ, 
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_NS_CPMG_2SITE_3D_FULL, 
MODEL_NS_CPMG_2SITE_STAR_FULL
+from specific_analyses.relax_disp.variables import EXP_TYPE_CPMG_SQ, 
MODEL_B14_FULL, MODEL_CR72, MODEL_CR72_FULL, MODEL_IT99, 
MODEL_NS_CPMG_2SITE_3D_FULL, MODEL_NS_CPMG_2SITE_STAR_FULL
 
 
 # Alter setup.
@@ -110,7 +110,7 @@
 Class Profile inherits the Dispersion container class object.
 
 
-def __init__(self, num_spins=1, model=None, r2=None, r2a=None, r2b=None, 
dw=None, pA=None, kex=None, spins_params=None):
+def __init__(self, num_spins=1, model=None, r2=None, r2a=None, r2b=None, 
dw=None, pA=None, kex=None, tex=None, spins_params=None):
 
 Special method __init__() is called first (acts as Constructor).
 It brings in data from outside the class like the variable num_spins.
@@ -168,7 +168,7 @@
 self.error.append([1.0]*len(cpmg_point))
 
 # Assemble param vector.
-self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b, 
dw=dw, pA=pA, kex=kex, spins_params=spins_params)
+self.params = self.assemble_param_vector(r2=r2, r2a=r2a, r2b=r2b, 
dw=dw, pA=pA, kex=kex, tex=tex, spins_params=spins_params)
 
 # Make nested list arrays of data. And return them.
 values, errors, cpmg_frqs, missing, frqs, exp_types, relax_times, 
offsets = self.return_r2eff_arrays()
@@ -292,7 +292,7 @@
 return values, errors, cpmg_frqs, missing, frqs, exp_types, 
relax_times, offsets
 
 
-def assemble_param_vector(self, r2=None, r2a=None, r2b=None, dw=None, 
pA=None, kex=None, spins_params=None):
+def assemble_param_vector(self, r2=None, r2a=None, r2b=None, dw=None, 
pA=None, kex=None, tex=None, spins_params=None):
 Assemble the dispersion relaxation dispersion curve fitting 
parameter vector.
 
 @keyword r2:The transversal relaxation rate.
@@ -333,6 +333,8 @@
 value = pA
 elif param_name == 'kex':
 value = kex
+elif param_name == 'tex':
+value = tex
 
 # Add to the vector.
 param_vector.append(value)
@@ -387,6 +389,8 @@
 yield 'pA', 0, 0
 elif param == 'kex':
 yield 'kex', 0, 0
+elif param == 'tex':
+yield 'tex', 0, 0
 
 
 def calc(self, params):
@@ -399,11 +403,11 @@
 
 
 # Return chi2 value.
-chi2 = self.model.func_CR72(params)
+chi2 = self.model.func_IT99(params)
 return chi2
 
 
-def single(num_spins=1, model=MODEL_CR72, iter=None):
+def single(num_spins=1, model=MODEL_IT99, iter=None):
 Calculate for a single spin.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -417,7 +421,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
tex=1/1000.0, spins_params=['r2', 'dw', 'pA', 'tex'])
 
 # Loop 100 times for each spin in the clustered analysis (to make the 
timing numbers equivalent).
 for spin_index in xrange(100):
@@ -427,7 +431,7 @@
 print(chi2 single:, chi2)
 
 
-def cluster(num_spins=100, model=MODEL_CR72, iter=None):
+def cluster(num_spins=2, model=MODEL_IT99, iter=None):
 Calculate for a number of clustered spins.
 
 @keyword num_spins: Number of spins in the cluster.
@@ -441,7 +445,7 @@
 
 
 # Instantiate class
-C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
kex=1000.0, spins_params=['r2', 'dw', 'pA', 'kex'])
+C1 = Profile(num_spins=num_spins, model=model, r2=5.0, dw=3.0, pA=0.9, 
tex=1/1000.0, spins_params=['r2', 'dw', 'pA', 'tex

r24142 - /branches/disp_spin_speed/lib/dispersion/mmq_cr72.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 20:22:02 2014
New Revision: 24142

URL: http://svn.gna.org/viewcvs/relax?rev=24142view=rev
Log:
Moved the eta_scale = 2.0**(-3.0/2.0) out of lib function for mmq cr72, since 
this is only needs to be computed once.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/mmq_cr72.py

Modified: branches/disp_spin_speed/lib/dispersion/mmq_cr72.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/mmq_cr72.py?rev=24142r1=24141r2=24142view=diff
==
--- branches/disp_spin_speed/lib/dispersion/mmq_cr72.py (original)
+++ branches/disp_spin_speed/lib/dispersion/mmq_cr72.py Wed Jun 18 20:22:02 2014
@@ -50,6 +50,9 @@
 # Python module imports.
 from numpy import arccosh, cos, cosh, isfinite, fabs, log, min, max, sin, 
sqrt, sum
 from numpy.ma import fix_invalid, masked_greater_equal, masked_where
+
+# Repetitive calculations (to speed up calculations).
+eta_scale = 2.0**(-3.0/2.0)
 
 
 def r2eff_mmq_cr72(r20=None, pA=None, dw=None, dwH=None, kex=None, 
cpmg_frqs=None, inv_tcpmg=None, tcp=None, back_calc=None):
@@ -130,7 +133,6 @@
 Dneg = 0.5 * (-1.0 + D_part)
 
 # Partial eta+/- values.
-eta_scale = 2.0**(-3.0/2.0)
 etapos_part = eta_scale * sqrt(Psi + sqrt_psi2_zeta2)
 etaneg_part = eta_scale * sqrt(-Psi + sqrt_psi2_zeta2)
 


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r24143 - /branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 20:23:51 2014
New Revision: 24143

URL: http://svn.gna.org/viewcvs/relax?rev=24143view=rev
Log:
Spell fix in code for ns cpmg 2site expanded.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py?rev=24143r1=24142r2=24143view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py   
(original)
+++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_expanded.py   Wed Jun 
18 20:23:51 2014
@@ -286,8 +286,7 @@
 k_BA = pA * kex
 k_AB = pB * kex
 
-
-# Repeditive calculations.
+# Repetitive calculations.
 half_tcp = 0.5 * tcp
 k_AB_plus_k_BA = k_AB + k_BA
 k_BA_minus_k_AB = k_BA - k_AB


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r24144 - /branches/disp_spin_speed/lib/dispersion/

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 20:28:05 2014
New Revision: 24144

URL: http://svn.gna.org/viewcvs/relax?rev=24144view=rev
Log:
Fix for missing comments.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py
branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py?rev=24144r1=24143r2=24144view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py   
(original)
+++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py   Wed Jun 
18 20:28:05 2014
@@ -141,7 +141,6 @@
 for si in range(NS):
 # Loop over the spectrometer frequencies.
 for mi in range(NM):
-
 # Extract the values from the higher dimensional arrays.
 R2A_si_mi=r20a[0, si, mi, 0, 0]
 R2B_si_mi=r20b[0, si, mi, 0, 0]

Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py?rev=24144r1=24143r2=24144view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_2site.py Wed Jun 18 
20:28:05 2014
@@ -301,7 +301,7 @@
 for mi in range(NM):
 # Loop over offsets:
 for oi in range(NO):
-
+# Extract parameters from array.
 r20a_i = R20A[si, mi, oi, 0]
 r20b_i = R20B[si, mi, oi, 0]
 dw_i = dw[si, mi, oi, 0]

Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py?rev=24144r1=24143r2=24144view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py Wed Jun 18 
20:28:05 2014
@@ -194,7 +194,7 @@
 for mi in range(NM):
 # Loop over offsets:
 for oi in range(NO):
-
+# Extract parameters from array.
 r20a_i = R20A[si, mi, oi, 0]
 r20b_i = R20B[si, mi, oi, 0]
 r20c_i = R20C[si, mi, oi, 0]

Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py?rev=24144r1=24143r2=24144view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_2site.py   Wed Jun 18 
20:28:05 2014
@@ -109,7 +109,7 @@
 for mi in range(NM):
 # Loop over offsets:
 for oi in range(NO):
-
+# Extract parameters from array.
 omega_i = omega[0, si, mi, oi, 0]
 offset_i = offset[0, si, mi, oi, 0]
 r1_i = r1[0, si, mi, oi, 0]

Modified: branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py?rev=24144r1=24143r2=24144view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py   (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_r1rho_3site.py   Wed Jun 18 
20:28:05 2014
@@ -130,7 +130,7 @@
 for mi in range(NM):
 # Loop over offsets:
 for oi in range(NO):
-
+# Extract parameters from array.
 omega_i = omega[0, si, mi, oi, 0]
 offset_i = offset[0, si, mi, oi, 0]
 r1_i = r1[0, si, mi, oi, 0]


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r24145 - in /branches/disp_spin_speed/lib/dispersion: ns_cpmg_2site_3d.py ns_cpmg_2site_star.py ns_mmq_3site.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 20:32:40 2014
New Revision: 24145

URL: http://svn.gna.org/viewcvs/relax?rev=24145view=rev
Log:
Fix for spaces aroung = outside functions.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py
branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py?rev=24145r1=24144r2=24145view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_3d.py Wed Jun 18 
20:32:40 2014
@@ -134,8 +134,8 @@
 for mi in range(NM):
 
 # Extract the values from the higher dimensional arrays.
-R2A_si_mi=r20a[0, si, mi, 0, 0]
-R2B_si_mi=r20b[0, si, mi, 0, 0]
+R2A_si_mi = r20a[0, si, mi, 0, 0]
+R2B_si_mi = r20b[0, si, mi, 0, 0]
 dw_si_mi = dw[0, si, mi, 0, 0]
 num_points_si_mi = int(num_points[0, si, mi, 0])
 

Modified: branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py?rev=24145r1=24144r2=24145view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py   
(original)
+++ branches/disp_spin_speed/lib/dispersion/ns_cpmg_2site_star.py   Wed Jun 
18 20:32:40 2014
@@ -142,8 +142,8 @@
 # Loop over the spectrometer frequencies.
 for mi in range(NM):
 # Extract the values from the higher dimensional arrays.
-R2A_si_mi=r20a[0, si, mi, 0, 0]
-R2B_si_mi=r20b[0, si, mi, 0, 0]
+R2A_si_mi = r20a[0, si, mi, 0, 0]
+R2B_si_mi = r20b[0, si, mi, 0, 0]
 dw_si_mi = dw[0, si, mi, 0, 0]
 num_points_si_mi = int(num_points[0, si, mi, 0])
 

Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py?rev=24145r1=24144r2=24145view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py Wed Jun 18 
20:32:40 2014
@@ -199,10 +199,10 @@
 r20b_i = R20B[si, mi, oi, 0]
 r20c_i = R20C[si, mi, oi, 0]
 
-dw_AB_i=dw_AB[si, mi, oi, 0]
-dw_AC_i=dw_AC[si, mi, oi, 0]
-dwH_AB_i=dwH_AB[si, mi, oi, 0]
-dwH_AC_i=dwH_AC[si, mi, oi, 0]
+dw_AB_i = dw_AB[si, mi, oi, 0]
+dw_AC_i = dw_AC[si, mi, oi, 0]
+dwH_AB_i =d wH_AB[si, mi, oi, 0]
+dwH_AC_i = dwH_AC[si, mi, oi, 0]
 num_points_i = num_points[si, mi, oi]
 
 # Populate the m1 and m2 matrices (only once per function call 
for speed).
@@ -377,10 +377,10 @@
 r20b_i = R20B[si, mi, oi, 0]
 r20c_i = R20C[si, mi, oi, 0]
 
-dw_AB_i=dw_AB[si, mi, oi, 0]
-dw_AC_i=dw_AC[si, mi, oi, 0]
-dwH_AB_i=dwH_AB[si, mi, oi, 0]
-dwH_AC_i=dwH_AC[si, mi, oi, 0]
+dw_AB_i = dw_AB[si, mi, oi, 0]
+dw_AC_i = dw_AC[si, mi, oi, 0]
+dwH_AB_i = dwH_AB[si, mi, oi, 0]
+dwH_AC_i = dwH_AC[si, mi, oi, 0]
 num_points_i = num_points[si, mi, oi]
 
 # Populate the m1 and m2 matrices (only once per function call 
for speed).


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r24146 - /branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 20:41:35 2014
New Revision: 24146

URL: http://svn.gna.org/viewcvs/relax?rev=24146view=rev
Log:
Critical fix for wrong space inserted in ns mmq 3site mq.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py

Modified: branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py?rev=24146r1=24145r2=24146view=diff
==
--- branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py (original)
+++ branches/disp_spin_speed/lib/dispersion/ns_mmq_3site.py Wed Jun 18 
20:41:35 2014
@@ -201,7 +201,7 @@
 
 dw_AB_i = dw_AB[si, mi, oi, 0]
 dw_AC_i = dw_AC[si, mi, oi, 0]
-dwH_AB_i =d wH_AB[si, mi, oi, 0]
+dwH_AB_i = dwH_AB[si, mi, oi, 0]
 dwH_AC_i = dwH_AC[si, mi, oi, 0]
 num_points_i = num_points[si, mi, oi]
 


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r24147 - /branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 20:41:37 2014
New Revision: 24147

URL: http://svn.gna.org/viewcvs/relax?rev=24147view=rev
Log:
Fixed the input for unit test of mmq cr72.

The number of input parameters has been lowered.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:

branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py

Modified: 
branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py?rev=24147r1=24146r2=24147view=diff
==
--- 
branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
(original)
+++ 
branches/disp_spin_speed/test_suite/unit_tests/_lib/_dispersion/test_mmq_cr72.py
Wed Jun 18 20:41:37 2014
@@ -62,7 +62,7 @@
 a = ones(self.ncyc.shape)
 
 # Calculate the R2eff values.
-r2eff_mmq_cr72(r20=self.r20*a, pA=self.pA, pB=pB, dw=dw_frq*a, 
dwH=dwH_frq*a, kex=self.kex, k_AB=k_AB, k_BA=k_BA, cpmg_frqs=self.cpmg_frqs, 
inv_tcpmg=self.inv_relax_times, tcp=self.tau_cpmg, back_calc=self.R2eff)
+r2eff_mmq_cr72(r20=self.r20*a, pA=self.pA, dw=dw_frq*a, dwH=dwH_frq*a, 
kex=self.kex, cpmg_frqs=self.cpmg_frqs, inv_tcpmg=self.inv_relax_times, 
tcp=self.tau_cpmg, back_calc=self.R2eff)
 
 # Check all R2eff values.
 for i in range(self.num_points):


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r24148 - /branches/disp_spin_speed/lib/dispersion/b14.py

[tlinnet]

Author: tlinnet
Date: Wed Jun 18 20:50:32 2014
New Revision: 24148

URL: http://svn.gna.org/viewcvs/relax?rev=24148view=rev
Log:
Added additional math domain checking in B14.

This is when v1c is less than 1.0.

Task #7807 (https://gna.org/task/index.php?7807): Speed-up of dispersion models 
for Clustered analysis.

Modified:
branches/disp_spin_speed/lib/dispersion/b14.py

Modified: branches/disp_spin_speed/lib/dispersion/b14.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/lib/dispersion/b14.py?rev=24148r1=24147r2=24148view=diff
==
--- branches/disp_spin_speed/lib/dispersion/b14.py  (original)
+++ branches/disp_spin_speed/lib/dispersion/b14.py  Wed Jun 18 20:50:32 2014
@@ -149,6 +149,7 @@
 t_max_e = False
 t_v3_N_zero = False
 t_log_tog_neg = False
+t_v1c_less_one = False
 
 # Catch parameter values that will result in no exchange, returning flat 
R2eff = R20 lines (when kex = 0.0, k_AB = 0.0).
 # Test if pA or kex is zero.
@@ -241,6 +242,13 @@
 # Real. The v_1c in paper.
 v1c = F0 * cosh(E0) - F2 * cos(E2)
 
+# Catch math domain error of sqrt of negative.
+# This is when v1c is less than 1.
+mask_v1c_less_one = v1c  1.0
+if any(mask_v1c_less_one):
+t_v1c_less_one = True
+v1c[mask_v1c_less_one] = 1.0
+
 # Exact result for v2v3.
 v3 = sqrt(v1c**2 - 1.)
 
@@ -286,6 +294,10 @@
 if t_max_e:
 back_calc[mask_max_e.mask] = r20a[mask_max_e.mask]
 
+# If v1c is less than 1.
+if t_v1c_less_one:
+back_calc[mask_v1c_less_one] = 1e100
+
 # If Tog_div is zero.
 if t_v3_N_zero:
 back_calc[mask_v3_N_zero] = 1e100


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